Methods and compositions to modulate antibiotic resistance and gastrointestinal microbiota

ABSTRACT

Disclosed herein are methods and compositions related to probiotic formulas. These formulas comprise the bacterial strain Lactobacillus crispatus WZ-12 or a derivative thereof. Other strains which can be included in the composition include, but are not limited to, Lactobacillus salivarius 1-14, or Lactobacillus reuteri 2-2, and derivatives thereof. These compositions can be used in a variety of methods to treat and/or ameliorate diseases, such as colonization of antibiotic-resistant bacteria in the host organism. Also disclosed herein are methods of treating those subjects in need thereof by administering the compositions disclosed herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of U.S. Provisional Application No. 62/729,031, filed Sep. 10, 2018, both of which are hereby incorporated herein by reference in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant No. 31-6025986 awarded by the US-UK Global Innovation Initiative through the U.S. Department of State. The Government has certain rights in the invention.

FIELD

The disclosure generally relates to the uses of bacterial strain isolates, and to improving the quality of intestinal microbiota and reducing the amount of antibiotic resistant bacteria therein.

BACKGROUND

The impact of antibiotics on the gastrointestinal (GI) tract is complicated partially due to the complexity of GI microbiota and the lack of appropriate markers to monitor. While pathogens have been the focus of antibiotic resistance studies for decades, pathogenic bacteria in particular constitute a very small percentage in GI microbiota (Laxminarayan et al., 2013). Targeting certain groups of commensal bacteria and tracking their dynamics during antibiotic treatment is a more promising strategy to explore antibiotic-GI tract interactions.

The rapid emergence and dissemination of antibiotic resistance (AR) is a critical threat to public health. Unnecessary use of antibiotics should be limited, particularly antibiotic growth-promoters in food-producing animal farming. Probiotics are an alternative to antibiotic use. The antimicrobial and microbiota-modulation activity of probiotics can hinder colonization of pathogenic bacteria, improve overall gut health, and potentially reduce the applied dosage of antibiotic (Vuotto et al., 2014). While the mainstream probiotics are primarily intended to modulate gut microbiota for controlling infections by pathogens and growth promotion, certain probiotic strains are also able to reduce the colonization of ART bacteria. For example, probiotic E. coli Nissle 1917 was observed to prevent the colonization of multidrug-resistant E. coli in human gut (Tannock et al., 2011). Other observed AR reduction activities include increasing strain susceptibility, inhibiting resistant gene transfer and performing antagonistic activity against AR strains (Moubareck et al., 2007; Ditu et al., 2011; Naderi et al., 2014). However, the mechanisms of mitigating AR by probiotics are not fully understood.

During early development of chickens hatched in a teaching farm, ampicillin resistance encoded by the bla_(CMY-2) gene has low abundance. However, the composition of GI microbiota is dynamic, affected not only by antibiotics but also by microorganisms ingested through oral routes (such as food, feed, water, etc.), as well as other host factors. Since antibiotic resistant (AR) bacteria are found in poultry gut microbiota with or without direct exposure to antibiotics, the large quantity of feces containing AR bacteria from poultry production represents an important contamination source impacting the environmental AR gene pool. Thus, targeted strategies to minimize the prevalence of AR in food-producing animal GI microbiota are essential for effective mitigation of AR in the poultry production system.

Probiotic development can include identifying novel probiotic candidates from commensal bacteria in gut microbiota, which may have better colonization capabilities and individual-specific benefits (Hill et al., 2014). The GI microbiota, including the pool of AR bacteria (sometimes referred to as resistome), are established at very early stage of life, which may be a desirable stage for effective probiotic intervention.

The compositions and methods disclosed herein address these and other needs.

SUMMARY

Disclosed herein is a feed composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof and an ingestible food product; wherein the composition comprises Lactobacillus crispatus WZ-12 or a derivative thereof in an amount sufficient for use as a probiotic treatment of a subject. Also disclosed is a pharmaceutical composition and an ingestible food product comprising the compositions disclosed herein.

Further disclosed is a method of modulating gut microbiota in a subject comprising administering a composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof to the subject.

Disclosed herein is a bacterial strain comprising a Lactobacillus crispatus WZ-12, Lactobacillus salivarius 1-14, or Lactobacillus reuteri 2-2 derivative engineered to comprise a derivative genome which differs from a parental genome of the parental strain by at least one nucleotide, and which improves one or more probiotic qualities of the engineered bacterial strain compared to the parental strain.

Additional aspects and advantages of the disclosure will be set forth, in part, in the detailed description and any claims which follow, and in part will be derived from the detailed description or can be learned by practice of the various aspects of the disclosure. The advantages described below will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate certain examples of the present disclosure and together with the description, serve to explain, without limitation, the principles of the disclosure. Like numbers represent the same element(s) throughout the figures.

FIG. 1 is an image showing predominant 16 S rRNA genes in total fecal DNA from chicken after 3 days of inoculation with Lactobacillus crispatus WZ-12 (alternatively referred to herein as Lactobacillus crispatus CG-12). Lane 1: Lactobacillus crispatus WZ-12; Lane 2: bla_(CMY-2) +E. coli marker strain; Lane 3: sample from control group; Lane 4-7: 4 individual samples from Lc-Saline group; Lane 8-13: 6 individual samples from Saline-Saline group.

FIG. 2 is an image showing predominant 16 S rRNA genes in total fecal DNA from chicken after 4 days of inoculation with bla_(CMY-2) +E. coli following lactobacillus inocula. Lane 1: Lactobacillus crispatus WZ-12; Lane 2: bla_(CMY-2) +E. coli marker strain. Lane 3: sample from control group; Lane 4-7: 4 individual samples from Lc-Saline group; Lane 8-13: 6 individual samples from Saline-Saline group.

FIG. 3A-C are images showing predominant bacterial population in chicken GI microbiota before, during and after antibiotic administration. The predominant GI bacterial population is shown for Day 20 before antibiotic treatment (FIG. 3A); on Day 21 during antibiotic treatment (FIG. 3B); and on Day 25 after antibiotic treatment (FIG. 3C). For each of FIG. 3A-3C, Lane 1: Lactobacillus crispatus WZ-12; Lane 2: bla_(CMY-2) +E. coli marker cocktail; Lane 3-6: 4 individual samples from Lc-Amp group; Lane 7-10: 4 individual samples from Saline-Amp group.

FIG. 4 is a graph showing the phylum distribution of GI microbiota at post-antibiotic treatment. Firmicutus and proteobacteria comprised the largest groups of GI microbiota, although other bacterial species not within these two groups were identified. Sets of columns on the left and second from left: 3 samples from Amp-Saline (AS) group on Day 25 (left) and Day 28 (second from left). Sets of columns third and fourth from the left: 3 samples from Amp-Lc (AL) group on Day 25 (third from left) and Day 28 (fourth from left).

FIGS. 5A and 5B show the impact of probiotic treatment on bacterial population in pooled feces of chickens. FIG. 5A) Phylum level; FIG. 5B) Class level. The treatments include Lane 1 (no, cocktail, no): no ESBL E. coli inoculation for 4 days, then inoculated with probiotic cocktail but no Tween 80; Lane 2 (no; no, no): no E. coli, no probiotics, no Tween 80; Lane 3: (probiotics, E. coli, no): probiotic cocktail for 4 days, followed by E. coli, but no Tween 80); Lane 4 (Yes, CG12, no): E. coli for 4 days, followed by Lb. crispatus (WZ12) for 4 days but no Tween 80; Lane 5 (yes, cocktail, no): E. coli for 4 days, followed by probiotic cocktail for 4 days, no Tween; Lane 6 ((yes, cocktail, yes): E. coli for 4 days, followed by probiotic cocktail for 4 days, with Tween 80; Lane 7 (Yes, no, no): E. coli for 4 days, saline for 4 days (no probiotics no Tween); Lane 8 (yes, no, yes): ESBL E. coli for 4 days, no probiotics but with Tween 80 for 4 days.

FIGS. 6A and 6B show probiotics and ESBL inoculation on the profiles of poultry fecal microbiota followed by oral or injective antibiotic treatment. FIG. 6A) Phylum level; FIG. 6B) Class level. Group 1: probiotic cocktail treatment throughout, E coli exposure from Day 5 for 4 days and then oral Amp; Group 2: probiotic/peanut butter treatment throughout followed by E coli exposure and then oral Amp; Group 3: inoculated (E coli) then exposed to oral Amp, Group 4: noninoculated then exposed to oral Amp, Group 5: noninoculated then exposed to injective Amp, Group 6: noninoculated then exposed to saline; Group 7: inoculated (E coli) then exposed to injective Amp.

FIG. 7A-E shows a krona chart of the composition of fecal microbiota on Day 25 in pooled samples. (A) NI-Saline-PO; (B) NI-Amp-IM; (C) NI-Amp-PO; (D) Amp-IM; (E) Amp-PO.

FIG. 8A-B shows growth inhibition tests. A). The “bully” E. coli of 0, 10-1, 10-2 dilutions inoculated on the LB plate covered with DH5a. B). Multiple DH5α derivatives M9-4-1 are no longer inhibited (clear inhibition zone) by the “bully” strain M9-4 but with white growth ring.

DETAILED DESCRIPTION

The following description of the disclosure is provided as an enabling teaching of the disclosure in its best, currently known embodiment(s). To this end, those skilled in the relevant art will recognize and appreciate that many changes can be made to the various embodiments of the invention described herein, while still obtaining the beneficial results of the present disclosure. It will also be apparent that some of the desired benefits of the present disclosure can be obtained by selecting some of the features of the present disclosure without utilizing other features. Accordingly, those who work in the art will recognize that many modifications and adaptations to the present disclosure are possible and can even be desirable in certain circumstances and are a part of the present disclosure. Thus, the following description is provided as illustrative of the principles of the present disclosure and not in limitation thereof.

Terminology

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs. The following definitions are provided for the full understanding of terms used in this specification.

Disclosed are the components to be used to prepare the disclosed compositions as well as the compositions themselves to be used within the methods disclosed herein. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutation of these compounds may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a particular bacterial strain is disclosed and discussed and a number of modifications that can be made to the bacterial strain are discussed, specifically contemplated is each and every combination and permutation of the bacterial strain and the modifications that are possible unless specifically indicated to the contrary. Thus, if a class of bacterial strains A, B, and C are disclosed as well as a class of bacterial strains D, E, and F and an example of a combination of bacterial strains, or, for example, a combination of bacterial strains comprising A-D is disclosed, then even if each is not individually recited each is individually and collectively contemplated meaning combinations, A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are considered disclosed. Likewise, any subset or combination of these is also disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E would be considered disclosed. This concept applies to all aspects of this application including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods.

It is understood that the compositions disclosed herein have certain functions. Disclosed herein are certain structural requirements for performing the disclosed functions, and it is understood that there are a variety of structures which can perform the same function which are related to the disclosed structures, and that these structures will ultimately achieve the same result.

Unless otherwise expressly stated, it is in no way intended that any method set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not actually recite an order to be followed by its steps or it is not otherwise specifically stated in the claims or descriptions that the steps are to be limited to a specific order, it is no way intended that an order be inferred, in any respect. This holds for any possible non-express basis for interpretation, including: matters of logic with respect to arrangement of steps or operational flow; plain meaning derived from grammatical organization or punctuation; and the number or type of embodiments described in the specification.

As used in the specification and claims, the singular form “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “an agent” includes a plurality of agents, including mixtures thereof.

As used herein, the terms “may,” “optionally,” and “may optionally” are used interchangeably and are meant to include cases in which the condition occurs as well as cases in which the condition does not occur. Thus, for example, the statement that a formulation “may include an excipient” is meant to include cases in which the formulation includes an excipient as well as cases in which the formulation does not include an excipient.

Ranges can be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another embodiment. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed.

As utilized herein, “probiotic” refers to microorganisms that form at least a part of the transient or endogenous flora and thereby exhibit a beneficial prophylactic and/or therapeutic effect on the host organism. Probiotics are generally known to be clinically safe (i.e., non-pathogenic) by those individuals skilled in the art.

The term “probiotic composition” refers to a composition comprising a probiotic bacterium in a pharmaceutically or nutraceutically acceptable carrier that allows high cell viability after oral administration. For example, in some cases, the probiotic bacterium is lyophilized. In some cases, the probiotic bacterium is encapsulated in a gel matrix.

The term “probiotic bacterium” denotes a natural or recombinant bacterium which ingested live in adequate quantities can exert beneficial effects on the human health. They are now widely used as a food additive for their health-promoting effects. Health benefits are a result of, for example, production of nutrients and/or co-factors by the probiotic, competition of the probiotic with pathogens and/or stimulation of an immune response in the subject by the probiotic.

The term “intestinal diseases,” as used herein, is intended to refer to bacterial infectious or inflammatory diseases in the intestine. Examples of the intestinal diseases include, but are not limited to, infectious diarrhea caused by pathogenic microorganisms (E. coli, salmonella, and clostridium), gastroenteritis, inflammatory bowel diseases, psychogenic enteritis syndrome, overgrowth of microorganisms in the small intestine, and the like.

As used herein, the terms “pathogen” and “parasite” are used interchangeably in the context of a deleterious organism growing in the gastrointestinal tract and/or feces of an animal, although it appreciated that these terms have distinctive meanings.

The term “encapsulate” refers to the coating of a probiotic or a plurality of probiotics in a composition. In one example, the probiotic is encapsulated in a composition that protects the probiotic from gastric conditions and, for example, that releases the probiotic in the intestine, such as the small intestine, of a subject.

The term “nutraceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are compatible with the other ingredients of the formulation and suitable for ingestion by mammals, such as humans.

The term “pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problems or complications commensurate with a reasonable benefit/risk ratio.

The term “prevent” refers to a treatment that forestalls or slows the onset of a disease or condition or reduces the severity of the disease or condition. Thus, if a treatment can treat a disease in a subject having symptoms of the disease, it can also prevent that disease in a subject who has yet to suffer some or all of the symptoms.

The term “subject” refers to any individual who is the target of administration or treatment. The subject can be a vertebrate, for example, a mammal. Thus, the subject can be a human or veterinary patient. The term “patient” refers to a subject under the treatment of a clinician, e.g., physician. The subject can be livestock, such as pigs, cows, goats, or poultry.

The term “therapeutically effective” refers to the amount of the composition used is of sufficient quantity to ameliorate one or more causes or symptoms of a disease or disorder. Such amelioration only requires a reduction or alteration, not necessarily elimination.

The term “treatment” refers to the medical management of a patient with the intent to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder. This term includes active treatment, that is, treatment directed specifically toward the improvement of a disease, pathological condition, or disorder, and also includes causal treatment, that is, treatment directed toward removal of the cause of the associated disease, pathological condition, or disorder. In addition, this term includes palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, pathological condition, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated disease, pathological condition, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated disease, pathological condition, or disorder.

As used herein, the term “probiotic bacterium” denotes a bacterium which ingested live in adequate quantities can exert beneficial effects on the human health.

By “normal gut flora” is meant a population of microbes that is substantially similar to the population of microbes present in the gut of a healthy control subject.

By “ameliorate” is meant decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease.

The term “comprising” as used herein is synonymous with “including” or “containing,” and is inclusive or open-ended and does not exclude additional, unrecited members, elements or method steps.

As used herein, the term “in vivo” refers to events that occur within an organism (e.g., animal, plant, or microbe).

As used herein, the term “isolated” refers to a substance or entity that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting), and/or (2) produced, prepared, and/or manufactured by the hand of man. Isolated substances and/or entities may be separated from at least about 10%, about 20%, about 30%>, about 40%>, about 50%>, about 60%), about 70%, about 80%>, about 90%>, or more of the other components with which they were initially associated. In some embodiments, isolated agents are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%), about 97%), about 98%>, about 99%, or more than about 99% pure. As used herein, a substance is “pure” if it is substantially free of other components.

The term “isolated bacterium” or “isolated polypeptide” is a polypeptide or bacteria that by virtue of its origin or source of derivation (1) is not associated with naturally associated components that accompany it in its native state, (2) exists in a purity not found in nature, where purity can be adjudged with respect to the presence of other cellular material (e.g., is free of other proteins from the same species) (3) is expressed by a cell from a different species, or (4) does not occur in nature (e.g., it is a fragment of a polypeptide found in nature or it includes amino acid analogs or derivatives not found in nature or linkages other than standard peptide bonds). Thus, a polypeptide that is chemically synthesized or synthesized in a cellular system different from the cell from which it naturally originates will be “isolated” from its naturally associated components. A polypeptide or bacteria may also be rendered substantially free of naturally associated components by isolation, using protein purification techniques well known in the art.

As used herein, a “modified derivative” refers to polypeptides or fragments thereof that are substantially homologous in primary structural sequence to a reference polypeptide sequence but which include, e.g., in vivo or in vitro chemical and biochemical modifications or which incorporate amino acids that are not found in the reference polypeptide. Such modifications include, for example, acetylation, carboxylation, phosphorylation, glycosylation, ubiquitination, labeling, e.g., with radionuclides, and various enzymatic modifications, as will be readily appreciated by those skilled in the art. A variety of methods for labeling polypeptides and of substituents or labels useful for such purposes are well known in the art, and include radioactive isotopes such as I, P, S, and H, ligands that bind to labeled antiligands (e.g., antibodies), fluorophores, chemiluminescent agents, enzymes, and antiligands that can serve as specific binding pair members for a labeled ligand. The choice of label depends on the sensitivity required, ease of conjugation with the primer, stability requirements, and available instrumentation. Methods for labeling polypeptides are well known in the art. See, e.g., Ausubel et al, Current Protocols in Molecular Biology, Greene Publishing Associates (1992, and Supplements to 2002).

As used herein, “polypeptide mutant” or “mutein” refers to a polypeptide whose sequence contains an insertion, duplication, deletion, rearrangement or substitution of one or more amino acids compared to the amino acid sequence of a reference protein or polypeptide, such as a native or wild-type protein. A mutein may have one or more amino acid point substitutions, in which a single amino acid at a position has been changed to another amino acid, one or more insertions and/or deletions, in which one or more amino acids are inserted or deleted, respectively, in the sequence of the reference protein, and/or truncations of the amino acid sequence at either or both the amino or carboxy termini. A mutein may have the same or a different biological activity compared to the reference protein.

In some embodiments, a mutein has, for example, at least 85% overall sequence homology to its counterpart reference protein. In some embodiments, a mutein has at least 90% overall sequence homology to the wild-type protein. In other embodiments, a mutein exhibits at least 95% sequence identity, or 98%, or 99%, or 99.5% or 99.9% overall sequence identity.

The term “polynucleotide”, “nucleic acid molecule”, “nucleic acid”, or “nucleic acid sequence” refers to a polymeric form of nucleotides of at least 10 bases in length. The term includes DNA molecules (e.g., cDNA or genomic or synthetic DNA) and R A molecules (e.g., mRNA or synthetic RNA), as well as analogs of DNA or RNA containing non-natural nucleotide analogs, non-native internucleoside bonds, or both. The nucleic acid can be in any topological conformation. For instance, the nucleic acid can be single-stranded, double-stranded, triple-stranded, quadruplexed, partially double-stranded, branched, hairpinned, circular, or in a padlocked conformation.

A “synthetic” RNA, DNA or a mixed polymer is one created outside of a cell, for example one synthesized chemically.

As used herein, an endogenous nucleic acid sequence in the genome of an organism (or the encoded protein product of that sequence) is deemed “recombinant” herein if a heterologous sequence is placed adjacent to the endogenous nucleic acid sequence, such that the expression of this endogenous nucleic acid sequence is altered. In this context, a heterologous sequence is a sequence that is not naturally adjacent to the endogenous nucleic acid sequence, whether or not the heterologous sequence is itself endogenous (originating from the same host cell or progeny thereof) or exogenous (originating from a different host cell or progeny thereof). By way of example, a promoter sequence can be substituted (e.g., by homologous recombination) for the native promoter of a gene in the genome of a host cell, such that this gene has an altered expression pattern. This gene would now become “recombinant” because it is separated from at least some of the sequences that naturally flank it.

A nucleic acid is also considered “recombinant” if it contains any modifications that do not naturally occur to the corresponding nucleic acid in a genome. For instance, an endogenous coding sequence is considered “recombinant” if it contains an insertion, deletion or a point mutation introduced artificially, e.g., by human intervention.

As used herein, the phrase “degenerate variant” of a reference nucleic acid sequence encompasses nucleic acid sequences that can be translated, according to the standard genetic code, to provide an amino acid sequence identical to that translated from the reference nucleic acid sequence. The term “degenerate oligonucleotide” or “degenerate primer” is used to signify an oligonucleotide capable of hybridizing with target nucleic acid sequences that are not necessarily identical in sequence but that are homologous to one another within one or more particular segments.

The term “percent sequence identity” or “identical” in the context of nucleic acid sequences refers to the residues in the two sequences which are the same when aligned for maximum correspondence. The length of sequence identity comparison may be over a stretch of at least about nine nucleotides, usually at least about 20 nucleotides, more usually at least about 24 nucleotides, typically at least about 28 nucleotides, more typically at least about 32, and even more typically at least about 36 or more nucleotides. There are a number of different algorithms known in the art which can be used to measure nucleotide sequence identity. For instance, polynucleotide sequences can be compared using FASTA, Gap or Bestfit, which are programs in Wisconsin Package Version 10.0, Genetics Computer Group (GCG), Madison, Wis. FASTA provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences. Pearson, Methods Enzymol. 183:63-98 (1990). For instance, percent sequence identity between nucleic acid sequences can be determined using FASTA with its default parameters (a word size of 6 and the NOP AM factor for the scoring matrix) or using Gap with its default parameters as provided in GCG Version 6.1, herein incorporated by reference. Alternatively, sequences can be compared using the computer program, BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990); Gish and States, Nature Genet. 3:266-272 (1993); Madden et al, Meth. Enzymol. 266: 131-141 (1996); Altschul et al, Nucleic Acids Res. 25:3389-3402 (1997); Zhang and Madden, Genome Res. 7:649-656 (1997)), especially blastp or tblastn (Altschul et al, Nucleic Acids Res. 25:3389-3402 (1997)).

The term “substantial homology” or “substantial similarity,” when referring to a nucleic acid or fragment thereof, indicates that, when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 76%, 80%>, 85%, or at least about 90%>, or at least about 95%, 96%, 97%, 98% or 99% of the nucleotide bases, as measured by any well-known algorithm of sequence identity, such as FASTA, BLAST or Gap, as discussed above.

Compositions

Antibiotic resistance is a major challenge to human health worldwide. The broad use of antibiotic resistance is considered the reason that led to the problem seen today. But innovative research discovered multiple key risk factors. Targeted mitigation of all is essential to achieve effective control of the antibiotic resistance problem, and also to protect human health and food animal production.

In contrast to general belief, it has been found that antibiotic resistant bacteria were abundant in feces from chicks hatched at teaching farm never been exposed to antibiotic treatments. The data illustrated that even if antibiotics were banned from applications in food animal production, the resistant bacteria population already existed in the system won't disappear without specific efforts. Animal feces is the largest reservoir for antibiotic resistant bacteria and resistance genes. Thus, targeted reduction of the antibiotic resistant gut bacteria becomes a priority for control the problem in food animal production.

Lactobacillus crispatus strain WZ-12 (alternatively referred to herein as Lactobacillus crispatus strain CG-12 herein) and multiple E. coli strains were originally isolated from gastrointestinal (GI) tracts of chickens. Being part of the natural microbiota, Lactobacillus crispatus WZ-12 has good colonization fitness in the chicken GI tract, especially during the early establishment of GI microbiota.

Lactobacillus crispatus WZ-12 strain is sensitive to ampicillin and doesn't carry the ampicillin resistance (AR) gene. It is also susceptible to many other antibiotics tested. In vitro assessments showed that Lactobacillus crispatus WZ-12 can inhibit the growth of various bacteria including ampicillin resistant E. coli. Thus, establishment of Lactobacillus crispatus WZ-12 in chicken GI tract at early stage of life may hinder the colonization of antibiotic resistant strains, resulting in a reduced antibiotic resistant population in the chicken GI tract and improve the gut health of the animals. This is critically important for mitigation of AR in the ecosystem.

Lactobacillus crispatus WZ-12 derivatives with increased minimum inhibitory concentration for multiple antibiotics are also contemplated in the present invention. Live cultures in various forms of Lactobacillus crispatus WZ-12 can be commercialized as a probiotic strain or part of the probiotic mix to poultry modulate gut health, improve animal health, and mitigate antibiotic resistance.

Also disclosed herein is a probiotic composition comprising the E. coli strain M9-4-1. The probiotic composition can further comprise Lactobacillus crispatus WZ-12, as well as other known probiotics, such as other strains of bacteria.

Further disclosed is a feed composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof and E. coli strain M9-4-1 or a derivative thereof and an ingestible food product; wherein the composition comprises Lactobacillus crispatus WZ-12 or a derivative thereof and E. coli strain M9-4-1 or a derivative thereof in an amount sufficient for use as a probiotic treatment of a subject.

It is understood that the compositions (comprising e.g., a probiotic bacteria) of the present disclosure can be used in combination with the various compositions, methods, products, and applications disclosed herein.

Disclosed herein is a feed composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof and an ingestible food product; wherein the composition comprises Lactobacillus crispatus WZ-12 or a derivative thereof in an amount sufficient for use as a probiotic treatment of a subject. Lactobacillus crispatus WZ-12 can be given alone, or with Lactobacillus salivarius 1-14 and/or Lactobacillus reuteri 2-2, for example. The bacterial strains disclosed herein (Lactobacillus crispatus WZ-12, Lactobacillus salivarius 1-14, and Lactobacillus reuteri 2-2 or derivatives thereof, for example) may be used alone or in together as a “probiotic” when given to humans or animals. The compositions disclosed herein can be embedded in the ingestible food product, so that the composition is coated or in a gel or other form that can be delivered in the ingestible food product to the subject. In one embodiment, the ingestible food product can retain the viability of the culture. An example of this is an emulsion of peanut butter comprising the composition disclosed herein.

By “Lactobacillus crispatus WZ-12 or a derivative thereof” is meant that the Lactobacillus crispatus WZ-12 may be genetically altered from its naturally occurring state, so that it possesses qualities or genetic elements which are not naturally occurring. For example, the bacteria may be recombinantly engineered to express nonendogenous genes, or may be engineered so that certain native genes are not expressed. The bacteria may be one that has been cultivated in the laboratory so that certain properties are enhanced, or may be genetically modified.

The microbes disclosed herein can be used or alone or in combination with antibiotic compounds or other functional anti-microbial drugs and supplements so as to form therapeutic compositions for use in ameliorating and/or controlling the colonization of pathogenic bacteria with the gastrointestinal tract of both humans and animals. In addition, these non-pathogenic, probiotic bacteria may be co-administered with an anti-fungal agent and/or an antibiotic to ameliorate the growth of the mycotic or bacterial pathogen in question. The compositions of the present invention may or may not be compounded with additional ingredients.

In brief, the present invention utilizes antibiotic-susceptible or antibiotic-tolerant but without transmissible AR genes, non-pathogenic bacteria to mitigate the growth and subsequent establishment of antibiotic-resistant, pathogenic microbes within, for example, the gastrointestinal tract. An example of an antibiotic resistant bacteria includes the ampicillin-resistant E. coli strains described herein. The antibiotic resistant bacteria can be multidrug resistant as well. Also disclosed herein are various therapeutic compositions, methods for using said therapeutic compositions, and systems for containing and administering/delivering said therapeutic compositions. Therefore, the probiotic treatment disclosed herein can be effective in reducing an amount of antibiotic resistant bacteria in a gut microbiota of the subject. By “reducing” is meant a 5, 10, 15, 20, 25, 30, 35, 40, 45 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% reduction in the amount of antibiotic resistant bacteria present in the gut microflora of a subject after having been administered the compositions disclosed herein.

In addition, the present invention also discloses compositions and methodologies for the utilization of these compositions, comprising non-pathogenic, probiotic lactic acid-producing bacteria, in the mitigation of the deleterious physiological effects of gastrointestinal tract pathogens, including antibiotic-resistant gastrointestinal tract pathogens, in both humans and animals, by the colonization (or more-correctly, re-colonization) of the gastrointestinal tract with probiotic microorganisms, following the administration of antibiotics, anti-fungal, anti-viral, and similar agents. The compositions disclosed herein demonstrate beneficial function within the gastrointestinal tract; and are non-pathogenic.

Throughout this specification the compositions of present invention may be referred to as a probiotic composition, a lactobacillus containing composition, a dietary supplement, or a food additive or ingestible product. All of these aforementioned terms mean a composition, regardless of form or the presence or absence of other ingredients, that contains viable or non-viable Lactobacillus crispatus WZ-12 or a derivative thereof as determined using the methods detailed herein.

The compositions disclosed herein may be taken orally as a bolus in the form of a gelatin capsule, pressed tablet, or gel cap. In another embodiment, the compositions of the present invention may be taken orally in the form of a liquid beverage. The liquid beverage may contain other ingredients such as, but not limited to flavor enhancers, sweeteners, viscosity enhancers and other food additives. The present invention may also be taken together with other foods either separately or compounded therewith.

In some embodiments, the composition is a foodstuff. In this regard, the term “foodstuff” as used herein includes liquids (e.g., drinks), semi-solids (e.g., gels, jellies, yogurt, etc.) and solids. Exemplary foodstuffs include dairy products, such as fermented milk products, unfermented mild products, yogurt, frozen yogurt, cheese, fermented cream, milk-based desserts milk powder, milk concentrate or cheese spread. Other products are also contemplated, such as soy-based products, oat-based products, peanut-based products, chocolate-based products, infant formula, and toddler formula.

The composition can also be presented in the form of a capsule, tablet, dried power, syrup, emulsion, etc. For example, the composition can be a pharmaceutical composition. Such a composition can comprise a pharmaceutically acceptable carrier, e.g., to facilitate the storage, administration, and/or the biological activity of the probiotic (see, e.g., Remington's Pharmaceutical Sciences, 16th Ed., Mac Publishing Company (1980). Suitable carriers for the present disclosure include those conventionally used, e.g., water, saline, aqueous dextrose, lactose, a buffered solution, starch, cellulose, glucose, lactose, sucrose, gelatin, malt, rice, flour, and the like. In some embodiments, the carrier provides a buffering activity to maintain the probiotic at a suitable pH to thereby exert a biological activity.

In a liquid therapeutic composition, the food-grade bacterium can be in suspension in a liquid that ensures physiological conditions for a probiotic bacterium. In a solid therapeutic composition, the food-grade bacterium can be present in free, preferably lyophilized form, or in immobilized form. For example, the food-grade bacterium can be enclosed in a gel matrix which provides protection for the cells.

The compositions disclosed herein can also be given to livestock in the form of a feed additive. For use as a feed additive, the composition may be formulated into a liquid with a high concentration of from 20 to 90%, or may be prepared as a powder or granules or emulsion. The feed additive may include at least one selected from the group consisting of an organic acid such as citric acid, fumaric acid, adipic acid, lactic acid, or malic acid, a phosphate salt such as sodium phosphate, potassium phosphate, acidic pyrophosphate, or polyphosphate (polymerized phosphate), and a natural antioxidant such as polyphenol, catechin, a-tocopherol, rosemary extract, vitamin C, green tea extract, licorice extract, chitosan, tannic acid, or phytic acid, various fatty acids, proteins, carbohydrates. The composition used as livestock feed may be formulated into various forms that are commonly used in the art with ingredients commonly used in livestock feed.

The feed additive and livestock feed may include grains such as powdered or pulverized wheat, oats, barley, corn, or rice; plant protein livestock feed containing rape, bean, or sunflower as a main ingredient; animal protein livestock feed such as blood powder, meat powder, bone powder, or fish powder; sugar; and dairy products such as powdered milk and whey powder. The feed additive and livestock feed may further include nutrient supplements, digestion- and absorption-assisting agents, growth promoting substances, or the like.

The livestock feed additive may be administered, alone or in combination with another edible excipient, to animals. In addition, the livestock feed additive may be administered as a top dressing to the livestock feed or as a mixture with the livestock feed, or in separate oral form. If the feed additive is administered separately from the livestock feed, it is combined with a pharmaceutically acceptable vehicle to prepare an immediate release or sustained release formulation. The edible vehicle may be solid or liquid, such as corn starch, lactose, sucrose, bean flake, peanut oil, olive oil, sesame oil, or propylene glycol. When a solid vehicle is used, the feed additive may be in the form of tablets, capsules, powder, troches or lozenges, or a non-dispersed top dressing. As for a liquid vehicle, the feed additive may be in the form of gelatin soft capsules, a syrup suspension, an emulsion, or a solution.

The livestock feed may include protein-containing organic cereal flour that is commonly used to satisfy the dietary demand of animals. The protein-containing cereal flour may comprise corn, bean flour, or a corn/bean flour mix.

In addition, the feed additive and livestock feed may include a supplement such as a preservative, a stabilizer, a wetting agent, an emulsifier, and a solubilizer. The feed additive may be added to the livestock feed in an infiltration, spraying, or mixing manner.

The compositions of the present invention can be administered to any animal in need of thereof including, but not limited to mammals, birds, reptiles and fish. Typical applications include administering the probiotic compositions of the present invention to humans, horses, swine (pigs), cows, sheep, dogs, cats, rabbits, chickens, turkeys, pheasants, quail, parakeets, parrots, and other wild and domesticated animals.

In one embodiment of the present invention, the composition is given as a dietary supplement. For example, when given to humans, the compositions disclosed herein can be given as a dietary supplement. Th dietary supplement, in one example, can comprise a gelatin capsule filled with the bacterial strain(s) disclosed herein. In another embodiment, the dietary supplement is in the form of a liquid preparation. In yet another embodiment of the present invention, the dietary supplement is in the form of an anal or vaginal suppository. When used as a suppository it may be formed into a convenient bolus and may contain non-toxic lubricants, stabilizers, waxes and the like to ease in the administration. In another embodiment of the present invention the lactobacillus dietary supplement may be compounded with foods such as, but not limited to dairy products, grains, breads, meats, fruits, vegetables, rice and the like. The form the lactobacillus dietary supplement of the present invention assumes is not important and is non-limiting.

It should also be noted that the present invention is not limited solely to oral administration of the compositions disclosed herein. For example, antibiotic and anti-fungal resistance is also associated with topical and intra-vaginal medications. Thus, in an additional embodiment, the co-administration of a beneficial bacterial culture with a vaginal anti-fungal medication would effectively aid in the mitigation of the mycotic or bacterial pathogen in question and repopulate the vagina and reduce the incidence of relapse. It should be noted that it has been demonstrated that the absence of lactic acid-producing bacteria within the vagina is the most common etiology of vaginal yeast infections and bacterial vaginosis.

In an additional embodiment, skin creams, lotions, gels and the like could similarly contain a beneficial biorational component that would be effective in controlling pathogenic organisms on the skin and further reduce the emergence of antibiotic resistant pathogens. By way of example, but not of limitation, the cells, spores or extracellular materials from such beneficial biorational bacteria could be incorporated into these skin products for this express purpose. Burn patients usually are given antibiotics to reduce the incidence of opportunistic infection. Pathogenic Pseudomonas, Staphylococcus, and/or Enterococci are frequently associated with infections of severe burns. Hence, the salves, lotions, gels and the like combined with the beneficial, biorational microorganisms or their extracellular products, as disclosed in the present invention, would be effective in achieving a state of proper biodiversity to the skin in burn cases, as, generally, such biodiversity is not associated with pathogenic overgrowth.

In one embodiment of the present invention the composition is freeze dried using standard methods known to those having ordinary skill in the art of food science. In another embodiment the composition of the present invention the composition is air-dried. In yet another embodiment the composition is a paste. In still another embodiment the composition of the present invention is a liquid.

In yet another specific embodiment, the Lactobacillus crispatus WZ-12 composition may be incorporated into an aqueous solution (e.g., physiological saline) for administration as a colonic, via an enema or the like) so as to directly administer the probiotic bacteria to the colon. This method of administration is highly efficacious for utilization of vegetative bacterial cells as they are not exposed to the highly acidic environment of the stomach as is the case during oral administration.

The composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof can comprise Lactobacillus crispatus WZ-12 or a derivative thereof in an amount from 1×10⁴ to 1×10⁷ colony forming units per milliliter. For example, the amount can be 1×10⁴, 1×10⁵, 1×10⁶, or 1×10⁷, or any amount in between, above, or below. The Lactobacillus crispatus WZ-12 compositions disclosed herein can contain sufficient colony-forming units (CFU) to compete with undesirable microorganisms, such as E. coli and Salmonella. The total amount consumed will depend on the individual needs of the animal and the weight and size of the animal. The preferred dosage for any given application can be easily determined by titration. Titration is accomplished by preparing a series of standard weight doses each containing from approximately 10⁵ to 10¹¹ bacteria per gram. A series of doses are administered beginning at 0.5 grams and continuing up to a logical endpoint determined by the size of the animal and the dose form. The appropriate dose is reached when the minimal amount of lactobacilli composition required to achieve the desired results is administered. The appropriate dose is also known to those skilled in the art as an “effective amount” of the probiotic compositions of the present invention.

The growth of the lactobacilli species disclosed herein to form cell cultures, cell pastes, and spore preparations is generally well-known within the art. It should be noted that the exemplary culture and preparative methods which are described herein may be readily utilized and/or modified for growth and preparation of other bacteria disclosed in the present invention.

The formulation for the composition disclosed herein may also include other probiotic agents or nutrients which promote spore germination and/or bacterial growth. For example, the Lactobacillus crispatus WZ-12 strain disclosed herein can be combined with a therapeutically-effective dose of an antibiotic. The therapeutic composition of the present invention may also contain approximately 1 to approximately 250 mg of the selected antibiotic per unit of composition. In preferred embodiments of the present invention, the Lactobacillus crispatus WZ-12 strain can combined with a therapeutic dose of an antibiotic such as Gentamicin; Vancomycin; Oxacillin; Tetracyclines; Nitrofurantoin; Chloramphenicol; Clindamycin; Trimethoprim-Sulfamethoxasole; a member of the Cephlosporin antibiotic family (e.g., Cefaclor, Cefadroxil, Cefixime, Cefprozil, Ceftriaxone, Cefuroxime, Cephalexin, Loracarbef, and the like); a member of the Penicillin family of antibiotics (e.g., Ampicillin, Amoxicillin/Clavulanate, Bacampicillin, Cloxicillin, Penicillin VK, and the like); with a member of the Fluoroquinolone family of antibiotics (e.g., Ciprofloxacin, Grepafloxacin, Levofloxacin, Lomefloxacin, Norfloxacin, Ofloxacin, Sparfloxacin, Trovafloxacin, and the like); or a member of the Macrolide antibiotic family (e.g., Azithromycin, Erythromycin, and the like).

The Lactobacillus crispatus WZ-12 strain can also be combined with a therapeutically-effective dose of an anti-fungal agent. The therapeutic composition of the present invention may also contain approximately 1 to 250 mg of the selected anti-fungal agent per unit of therapeutic composition. Typical anti-fungal agents which may be utilized include, but are not limited to: Clotrimazole, Fluconazole, Itraconazole, Ketoconazole, Miconazole, Nystatin, Terbinafine, Terconazole, Tioconazole, and the like.

The Lactobacillus crispatus WZ-12 compositions of the present invention may also include known antioxidants, buffering agents, and other agents such as coloring agents, flavorings, vitamins or minerals. For example, a preferred therapeutic composition may also contain one or more of the following minerals: calcium citrate (15-350 mg); potassium gluconate (5-150 mg); magnesium citrate (5-15 mg); and chromium picollinate (5-200 μg). In addition, a variety of salts may be utilized, including calcium citrate, potassium gluconate, magnesium citrate and chromium picollinate. Thickening agents may be added to the compositions such as polyvinylpyrrolidone, polyethylene glycol or carboxymethylcellulose. Preferred additional components of a therapeutic composition of this invention can include assorted colorings or flavorings, vitamins, fiber, enzymes and other nutrients. Preferred sources of fiber include any of a variety of sources of fiber including, but not limited to: psyllium, rice bran, oat bran, corn bran, wheat bran, fruit fiber and the like. Dietary or supplementary enzymes such as lactase, amylase, glucanase, catalase, and the like enzymes can also be included. Chemicals used in the present compositions can be obtained from a variety of commercial sources, including Spectrum Quality Products, Inc (Gardena, Calif.), Sigma Chemicals (St. Louis, Mich.), Seltzer Chemicals, Inc., (Carlsbad, Calif.) and Jarchem Industries, Inc., (Newark, N.J.).

The various active agents (e.g., probiotic bacteria, antibiotics, anti-fungal agents, bifidogenic oligosaccharides, and the like) are combined with a carrier which is physiologically compatible with the gastrointestinal tissue of the species to which it is administered. Carriers can be comprised of solid-based, dry materials for formulation into tablet, capsule or powdered form; or the carrier can be comprised of liquid or gel-based materials for formulations into liquid or gel forms. The specific type of carrier, as well as the final formulation depends, in part, upon the selected route(s) of administration.

The Lactobacillus crispatus WZ-12 composition of the present invention may also include a variety of carriers and/or binders. A preferred carrier is micro-crystalline cellulose (MCC) added in an amount sufficient to complete the one gram dosage total weight. Particularly preferred formulations for a therapeutic composition of this invention will be described, infra. Carriers can be solid-based dry materials for formulations in tablet, capsule or powdered form, and can be liquid or gel-based materials for formulations in liquid or gel forms, which forms depend, in part, upon the routes of administration.

Typical carriers for dry formulations include, but are not limited to: trehalose, malto-dextrin, rice flour, micro-crystalline cellulose (MCC) magnesium sterate, inositol, FOS, GOS, dextrose, sucrose, and like carriers. Where the composition is dry and includes evaporated oils that produce a tendency for the composition to cake (adherence of the component spores, salts, powders and oils), it is preferred to include dry fillers which distribute the components and prevent caking. Exemplary anti-caking agents include MCC, talc, diatomaceous earth, amorphous silica and the like, and are typically added in an amount of from approximately 1% to 95% by weight. It should also be noted that dry formulations which are subsequently rehydrated (e.g., liquid formula) or given in the dry state (e.g., chewable wafers, pellets or tablets) are preferred to initially hydrated formulations. Dry formulations (e.g., powders) may be added to supplement commercially available foods (e.g., liquid formulas, strained foods, or drinking water supplies). Similarly, the specific type of formulation depends upon the route of administration.

Suitable liquid or gel-based carriers include but are not limited to: water and physiological salt solutions; urea; alcohols and derivatives (e.g., methanol, ethanol, propanol, butanol); glycols (e.g., ethylene glycol, propylene glycol, and the like). Preferably, water-based carriers possess a neutral pH value (i.e., pH 7.0). The compositions may also include natural or synthetic flavorings and food-quality coloring agents, all of which must be compatible with maintaining viability of the microorganism. Well-known thickening agents may also be added to the compositions such as corn starch, guar gum, xanthan gum, and the like. By way of example and not of limitation, preferred inhibitors include: hyper-saline carriers, methylparaben, guargum, polysorbates, preservatives, and the like.

Preservatives may also be included within the carrier including methylparaben, propylparaben, benzyl alcohol and ethylene diamine tetraacetate salts. Well-known flavorings and/or colorants may also be included within the carrier. The compositions of the present invention may also include a plasticizer such as glycerol or polyethylene glycol (with a preferred molecular weight of MW=800 to 20,000). The composition of the carrier can be varied so long as it does not interfere significantly with the pharmacological activity of the active ingredients.

When used as a dietary supplement or foodstuff, the composition can include any of a variety of nutritional agents, as are well known, including vitamins, minerals, essential and non-essential amino acids, carbohydrates, lipids, foodstuffs, dietary supplements, and the like. Preferred compositions comprise vitamins and/or minerals in any combination. Vitamins for use in a composition of this invention can include vitamins B, C, D, E, folic acid, K, niacin, and like vitamins. The composition can contain any or a variety of vitamins as may be deemed useful for a particularly application, and therefore, the vitamin content is not to be construed as limiting. Typical vitamins are those, for example, recommended for daily consumption and in the recommended daily amount (RDA), although precise amounts can vary. The composition would preferably include a complex of the RDA vitamins, minerals and trace minerals as well as those nutrients that have no established RDA, but have a beneficial role in healthy human or animal physiology. The preferred mineral format would include those that are in either the gluconate or citrate form because these forms are more readily metabolized by lactobacilli. In a related embodiment, the invention contemplates a composition comprising a viable Lactobacillus crispatus WZ-12 composition in combination with any material to be adsorbed, including but not limited to nutrient supplements, foodstuffs, vitamins, minerals, medicines, therapeutic compositions, antibiotics, hormones, steroids, and the like compounds where it is desirable to insure efficient and healthy absorption of materials from the gastrointestinal track into the blood. The amount of material included in the composition can vary widely depending upon the material and the intended purpose for its absorption, such that the invention is not to be considered as limiting. Other components of the compositions of the present invention can be a bifidogenic oligosaccharide, as described herein.

As mentioned above, the composition disclosed herein can comprise more than one probiotic bacteria. For example, the composition can comprise Lactobacillus salivarius 1-14 or a derivative thereof, or Lactobacillus reuteri 2-2 or a derivative thereof. The composition can comprise two or more bacteria selected from the group consisting of Lactobacillus crispatus WZ-12 or a derivative thereof, Lactobacillus salivarius 1-14 or a derivative thereof, or Lactobacillus reuteri 2-2 or a derivative thereof.

Methods

Disclosed herein is a method of modulating gut microbiota in a subject comprising administering a composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof to the subject. The disclosed methods of treatment function so as to inhibit the growth of the pathogenic bacteria which are associated with gastrointestinal infections, as well as to concomitantly mitigate the deleterious physiological effects/symptoms of these pathogenic infections.

The amount of antibiotic resistant bacteria in a gut microbiota of the subject can be determined after the administration step. For example, such determination can comprise measuring an amount of bla_(CMY-2) or other antibiotic resistance gene(s) in a fecal sample of the subject.

The compositions disclosed herein can be used to modulate gut microflora in a variety of ways, which can be customized to the subject receiving the treatment. For example, the treatment can occur in 2, 3, 4, 5, 6, 7, or more doses. The doses can be given once every day, or can be administered multiple times throughout the same day. One of skill in the art will appreciate that the doses can be administered in a variety of ways. The compositions disclosed herein can be administered in utero, or in the case of fowl, in ovo, or can be given upon birth, or 1, 2, 3, 4, 5, 6, 7, or more days after birth. The compositions can be administered to adults as a routine additive, or can be administered on an as-needed basis.

Disclosed herein is a bacterial strain comprising a Lactobacillus crispatus WZ-12, Lactobacillus salivarius 1-14, or Lactobacillus reuteri 2-2 derivative engineered to comprise a derivative genome which differs from a parental genome of the parental strain by at least one nucleotide, and which improves one or more probiotic qualities of the engineered bacterial strain compared to the parental strain. In one example, the derivative lacks a mobile genetic element present in the parental strain. The mobile genetic element can comprise a phage polynucleotide or an integron polynucleotide encoding one or more polypeptides capable of facilitating horizontal gene transfer. The derivative can lack a polynucleotide encoding an antibiotic resistance polypeptide present in the parental strain.

The derivative can have the improved quality comprises increased modulation of a gut microbiota in a subject as compared to the parental strain. The increased modulation can comprise colonizing the gut microbiota of the subject for a greater duration than the parental strain. The increased modulation can comprise reducing the amount of antibiotic resistant bacteria in the gut microbiota of the subject more than the parental strain.

Probiotic lactic acid bacterium, including Lactobacillus crispatus, are generally regarded as safe by those skilled within the art (i.e., GRAS Certified by the FDA) and, therefore, suitable for direct ingestion in food stuffs or as a food supplement. The methods of the present invention comprise administration of a therapeutic composition containing Lactobacillus crispatus WZ-12 or a derivative thereof to the gastrointestinal tract of a human or animal, to treat or prevent bacterial infection. Administration is preferably made using a liquid, powder, solid food and the like formulation compatible with oral administration, all formulated to contain a therapeutic composition of the present invention by use of methods well-known within the art.

The methods of the present invention include administration of Lactobacillus crispatus WZ-12 or a derivative thereof to a human or animal, so as to treat or prevent the colonization of antibiotic-resistant pathogens with the gastrointestinal tract. In particular, for VRE, VISA, PRP, and other pathogens, the methods include administering to the patient, for example, Lactobacillus crispatus WZ-12 or a derivative thereof in food or as a food supplement. Oral administration is preferably in an aqueous suspension, emulsion, powder or solid, either already formulated into a food, or as a composition which is added to food by the user prior to consumption. Administration to the gastrointestinal tract may also be in the form of an anal suppository (e.g., in a gel or semi-solid formulation). All such formulations are made using standard methodologies.

Administration of a therapeutic composition is preferably to the gastrointestinal tract using a gel, suspension, aerosol spray, capsule, tablet, powder or semi-solid formulation (e.g., a suppository) containing a therapeutic composition of the present invention, all formulated using methods well-known within the art. Of course, the specific route, dosage and timing of the administration will depend, in part, upon the particular pathogen and/or condition being treated, as well as the extent of said condition.

The present invention further contemplates a therapeutic system for treating, reducing and/or controlling pathogenic bacterial infections. Typically, the system is in the form of a package containing a therapeutic composition of the present invention, or in combination with packaging material. The packaging material includes a label or instructions for use of the components of the package. The instructions indicate the contemplated use of the packaged component as described herein for the methods or compositions of the invention.

By way of example, and not of limitation, a system can comprise one or more unit dosages of a therapeutic composition according to the present invention. Alternatively, the system can alternately contain bulk quantities of a therapeutic composition. The label contains instructions for using the therapeutic composition in either unit dose or in bulk forms as appropriate, and may also include information regarding storage of the composition, disease indications, dosages, routes and modes of administration and the like information.

EXAMPLES

To further illustrate the principles of the present disclosure, the following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compositions, articles, and methods claimed herein are made and evaluated. They are intended to be purely exemplary of the invention and are not intended to limit the scope of what the inventors regard as their disclosure. These examples are not intended to exclude equivalents and variations of the present invention which are apparent to one skilled in the art. Unless indicated otherwise, temperature is ° C. or is at ambient temperature, and pressure is at or near atmospheric. There are numerous variations and combinations of process conditions that can be used to optimize product quality and performance. Only reasonable and routine experimentation will be required to optimize such process conditions.

Example 1 Abstract

The gastrointestinal (GI) microbiota consists of a large number of bacterial cells, but less than 1% are cultivable. Nevertheless, cultivable bacteria provide important information on GI ecology, including the profile of antibiotic resistance (AR). This example identifies several culture-recovered commensal bacterial strains isolated from chicken feces, and examines their potential contribution to AR ecology. Three Amp^(r) E. coli (E. coli CA-1 or y M9-1 elsewhere, E. coli CA-4 or elsewhere M9-4 and E. coli CA-20 or M9-12 elsewhere) strains were identified as resistant to β-lactam, erythromycin, daptomycin, vancomycin and linezolid antibiotics, but susceptible to tetracycline and quinolone antibiotics. Lactobacillus crispatus WZ-12 (sometimes referred to simply as “WZ-12”) was isolated and susceptible to most antibiotics examined, but resistant to quinolone and daptomycin. The result was consistent with data by whole genome sequence analysis.

Materials and Methods

Bacterial Strains.

Multiple Amp^(r) strains from feces of broiler chickens without antibiotic treatment were recovered on Columbia blood Agar base (Becton, 100 Dickinson and Company, Franklin Lakes, N.J.) supplemented with 5% defibrinated sheep blood (Thermo Scientific™, Grand Island, N.Y.). The strains were maintained in Columbia broth (Becton Dickinson and Company, Franklin Lakes, N.J.), and propagated by aerobic growth at 37° C., and further subjected to strain identification and Minimum Inhibition Concentration (MIC) assessments.

Multiple commensal bacterial strains from chicken feces were recovered from Columbia blood Agar base (Becton, 100 Dickinson and Company, Franklin Lakes, N.J.) supplemented with 5% defibrinated sheep blood (Thermo Scientific™, Grand Island, N.Y.), and maintained in Columbia broth (Becton Dickinson and Company, Franklin Lakes, N.J.) and propagated by anaerobic growth at 37° C. The strains were subjected to antibiotic susceptibility assessment followed by strain identification.

Screening of Antibiotic Susceptible Commensal Strains.

Recovered commensal strain isolates (over 1000 colonies) were spotted on Columbia broth (Becton, 100 Dickinson and Company, Franklin Lakes, N.J.) agar plates containing each of the four antibiotics for rapid assessment of phenotypic resistance profiles. Screened antibiotics included 16 m/mL tetracycline (Sigma-Aldrich, St. Louis, Mo., USA), 100 m/mL erythromycin (Fisher Scientific, Waltham, Mass., USA), 32 m/mL ampicillin (Sigma-Aldrich), and 152 m/mL sulfamethoxazole (Sigma-Aldrich) with 8 m/mL trimethoprim (Sigma-Aldrich).

Strain Identification.

Phylotype identity and AR determinants were examined by conventional PCR. Primers used for identification and gene screening are listed in Table 1 and were synthesized by Sigma-Aldrich. The sequence of the 16 S rRNA amplicon was confirmed by DNA sequencing at the Plant Microbe Genomics Facility of the Ohio State University and compared with published AR gene sequences deposited in the NCBI database. An API® 50 CH (Biomerieus, Durham, N.C., US) identification strip was used for further identification of Lactobacillus.

TABLE 1 Primers used in strain identification. Amplicon Primer Sequence size size Reference bla_(CMY-2) FP GACAGCCTCTTTC 1,143 bp (Zhao and TCCACA others, 2001) bla_(CMY-2) RP TGGAACGAAGGCT ACGTA 16S-357F- CGCCCGCCGCGCG   233 bp (Muyzer and GC CGGCGGGCGGGGC others, 1993) GGGGGCACGGGGG GCCTACGGGAGGC AGCAG 16S-518R ATTACCGCGGCTG CTGG FP: forward primer; RP: reversed primer (SEQ ID NOS: 1-6, respectively)

Minimum Inhibition Concentration (MIC) Assessment.

A TREK Sensititre diagnostic system (Thermo scientific, Oakwood Village, Ohio, USA) was used to assess the AR phenotype and MIC of isolated strains. Protocols to use this system can be found on www.trekds.com. Cation-adjusted Mueller Hinton Broth (Becton, Dickinson and Company, MD, USA) was used as basic medium.

Shotgun Whole Genome Sequencing, Assembly and Annotation.

DNA of Lactobacillus crispatus WZ-12 was extracted from a colony using an UltraClean® Microbial DNA Isolation Kit (Mo Bio Laboratories Inc; Carlsbad, Calif., USA). DNA was sent to the Nationwide Children's hospital (Columbus, Ohio USA) for sequencing on an Illumina HiSeq 2500 system (Illumina Inc; San Diego, Calif., USA). Assembly of bacterial genome was performed using CLC Genomics Workbench 9.0 (CLC bio; Katrinebjerg, Denmark). Reference mapping of reads was performed using the genome of the Lactobacillus crispatus ST1 (GenBank accession no. FN692037.1). The assembled contigs were aligned to the Comprehensive Antibiotic Resistance Database (CARD) to search for AR determinants (McArthur et al., 2013). Annotation of the assembled contigs was performed on the RAST (Rapid Annotation using Subsystem Technology) server (Aziz et al., 2008; Overbeek et al., 2014; Brettin et al., 2015).

Results

Identification and Characterization of E. coli Strains.

NCBI blast results of the 16 S rRNA sequence from the Amp^(r) strains showed that all three strains of interest had 100% query coverage and over 98% sequence identity to the E. coli 16 S rRNA sequences in NCBI database. The three strains were designated as E. coli CA-1 (M9-1 elsewhere), E. coli CA-4 (M9-4 elsewhere), E. coli CA-20 (M-12 elsewhere). All three E. coli strains were bla_(CMY-2) ⁺ by conventional PCR. The bla gene encodes β-lactamase, an enzyme which cleaves β-lactam antibiotics, thereby conferring resistance to this class of antibiotics (including ampicillin). MIC assessments results of the E. coli strains were listed in Table 2. The MIC profiles of E. coli CA-1 AND E. coli CA-4 were highly identical. Three Amp^(r) E. coli had high resistance to β-lactam antibiotics (except for ceftriaxone), for example penicillin, ampicillin and oxacillin. Only E. coli CA-20 had some resistant to ceftriaxone. The E. coli strains were also resistant to erythromycin and some peptide antibiotics (daptomycin, vancomycin and linezolid). But they had low MIC values for tetracycline and quinolones, indicating susceptibility to these two categories of antibiotics.

Identification and Characterization of Commensal Lactobacillus Strains.

Among over 1,000 strains examined, a strain was isolated which was susceptible to ampicillin, tetracycline, erythromycin and sulfonamide/trimethoprim. The strain was named CG-12 (referred to herein as WZ-12, alternatively) and originated from Leghorn chicken. CG-12 was identified to be Lactobacillus by 16 S rRNA gene sequence assessment without a confirmed species. The API® 50CH result indicated the tested susceptible strain had 99.9% possibility to be Lactobacillus crispatus. This strain was thus designated as Lactobacillus crispatus CG-12. Lactobacillus crispatus CG-12 was bla_(CYM-2) ⁻ by PCR, indicating the absence of a β-lactam resistance gene. Lactobacillus crispatus CG-12 had low MIC values for most tested antibiotics (Table 2), but was resistant to daptomycin and quinolone (levofloxacin, gatifloxacin and ciprofloxacin).

TABLE 2 MIC of selected antibiotics for E. coli CA-1, E. coli CA-4, E. coli CA-20 and Lactobacillus crispatus CG-12. L. crispatus Antibiotic E.coli CA-1 E.coli CA-4 E.coli CA-20 CG-12 ERY >4 >4 >4 <0.25 CLI >2 >2 >2 <0.12 SYN >4 >4 >4 0.25 DAP >8 >8 >8 4 VAN >128 >128 >128 <1 TET <2 <2 <2 <2 AMP >16 >16 >16 0.5 GEN 4 4 8 16 LEVO <0.25 <0.25 <0.25 >8 LZD >8 >8 >8 2 AXO <8 <8 16 <8 STR <1000 <1000 <1000 <1000 PEN >8 >8 >8 0.5 RIF 4 >4 4 1 GAT <1 <1 <1 4 CIP <0.5 <0.5 <0.5 >2 SXT <0.5/9.5 <0.5/9.5 <0.5/9.5 2/38 OXA+ >8 >8 8 <0.25 MIC values are expressed in μg/mL. ERY: erythromycin; CLI: clindamycin; SYN: quinupristin/dalfopristin; DAP: daptomycin; VAN: vancomycin; TET: tetracycline; AMP: ampicillin; GEN: gentamicin; LEVO: levofloxacin; LZD: linezolid; AXO: ceftriaxone; STR: streptomycin; PEN: penicillin; RIF: rifampin; GAT: gatifloxacin; CIP: ciprofloxacin; SXT: sulfamethoxazole/trimethoprim; OXA+: oxacillin+2% NaC.

Whole genome sequence assessment of Lactobacillus crispatus CG-12. A total of 63 contigs longer than 1,000 bps were assembled from sequence data with a total length of 2,046,783 bp. Compared to a Genebank reference strain (Lactobacillus crispatus ST1, Genebank sequence No. FN692037.1), full length chromosomal genome (2,043,161 bp), the sequence coverage was nearly complete.

Two AR-related gene sequences were detected in the scaffold genome when compared to CARD database. A 346 bp sequence that had 77% identity to Staphylococcus aureus parE gene was observed on Contig 11 (153,379 bp). It encoded DNA topoisomerase IV subunit B, which confers resistance to aminocoumatin and fluoroquinolones. Another 737 bp sequence that had 73% identity to Staphylococcus aureus rpoC was located on Contig 22 (65,018 bp). It encoded DNA-directed RNA polymerase β-subunit and confers resistance to distamycin. These results were consistent with MIC tests.

RAST server annotations indicated there were phage-related genes in the genome of Lactobacillus crispatus CG-12. Phage related genes include phage replication initiation protein, phage anti-repressor protein, phage integrase, phage immunity repressor, among others.

Discussion and Conclusions

Strain identification is important in the study of antibiotic resistance in commensal microbiota. Bacterial strain prevalence and AR profile is a good indication of the overall AR status in the microbiota.

Three Amp^(r) isolates were identified and determined to be Escherichia coli. The AR gene bla_(CMY-2) was detected in all three strains. These E. coli strains had high resistance to β-lactam antibiotics according to the MIC test. Similarity in MIC profile observed between E. coli CA-1 and E. coli CA-4 indicated these two strains may be identical.

An ampicillin-susceptible strain CG-12 was identified as Lactobacillus crispatus. Lactobacillus crispatus is a commensal bacterial species prevalent in neonatal GI microbiota. Lactobacillus crispatus CG-12 was susceptible to most tested antibiotics but has relatively high resistance to quinolone antibiotics and daptomycin. This result is consistent with whole genome sequence analysis, as sequences with high homology to the parE and rpoC genes were observed in the CG-12 genome. Other beta-lactam resistance genes were not observed. The presence of phage-related genes indicates that gene transfer activity was potentially involved during the evolution of this strain.

The three bla_(CMY-2) ⁺ E. coli strains have high resistance to β-lactams and can be used as indicators for responses to ampicillin selective pressure. The commensal bla_(CMY-2) ⁻ Lactobacillus crispatus CG-12 has low resistance to most commonly used antibiotics and no Amp^(r) gene was detected on its genome. Thus, CG-12 is useful for probiotic methods of countering AR strains in GI microbiota.

Example 2 Abstract

Antibiotic-susceptible Lactobacillus crispatus strain CG-12 was isolated and characterized for antibiotic susceptibility profiles and whole genome sequencing. In vitro studies showed the strain can inhibit the growth of bla_(CMY-2) +E. coli strains, isolated from natural chicken fecal microbiota. Lactobacillus crispatus CG-12 was examined in vivo using a chicken model to test colonization resistance against bla_(CMY-2) +E. coli in gut microbiota. Lactobacillus crispatus CG-12 reduced the prevalence of the bla_(CMY-2) gene in newly established GI microbiota. Pre-inoculation of Lactobacillus crispatus CG-12 at an early stage didn't prevent colonization by AR E. coli. 10 days of inoculation of Lactobacillus crispatus CG-12 had little effect on eliminating the particularly targeted (inoculated) AR bacteria and reducing AR proliferation during antibiotic challenge. Post-antibiotic administration of Lactobacillus crispatus CG-12 did not significantly recover the diversified constitution of GI microbiota. Thus, administration of Lactobacillus crispatus CG-12 significantly reduced the early establishment of the bla_(CMY-2) gene pool, but had limited impact on AR E. coli from colonization to proliferation. This example shows that Lactobacillus crispatus was prevalent in neonatal GI microbiota of chicken, and that antibiotic-susceptible Lactobacillus crispatus CG-12 reduced early establishment of the AR gene pool.

Materials and Methods

Bacterial strains and culture preparation. Three bla_(CMY-2) ⁺ Escherichia coli strains were isolated from feces of two 4-day-old broiler chickens. E. coli strains were incubated separately in Columbia Broth (Becton, 100 Dickinson and Company, Franklin Lakes, N.J.) at 37° C. Lactobacillus crispatus CG-12 was isolated from feces of 3-week-old Leghorn chickens, and was incubated in MRS broth (Becton, 100 Dickinson and Company, Franklin Lakes, N.J.) at 37° C. For inocola preparations, 1 mL of overnight culture was precipitated by centrifugation (8000×g, 1 minute), washed and re-suspended in 1 mL saline. A cocktail of three E. coli strains for inoculation was prepared by mixing the cell suspension of designated strains and standardized to 10⁶ CFU/mL per each strain.

Growth Inhibition Assessments: Agar Diffusion.

Bacterial competition assays were performed in a 1×3 matrix format by an agar diffusion technique (Durso et al., 2004). Supernatant producer and receptor strains were grown overnight in MRS at 37° C. anaerobically. Producer strain culture was centrifuged at 10000×g for 5 min, and the supernatants were filtered by 0.22 mm filter to remove remaining cells. Receptor strain cells were inoculated into tempered soft Columbia agar (20 μl of cells culture into 3 mL soft agar) and overlaid onto Columbia agar plates. Three sterile 6-mm-diameter paper disks were placed on the agar in each plate, and 25 μl of each supernatant was inoculated onto each disk. Plates were incubated anaerobically overnight at 37° C. Zones of clearance were recorded in millimeters.

Growth Inhibition Assessments: Efficacy of Inhibition by Metabolites.

Overnight cultures of three E. coli strains (10⁶ CFU/mL) were mixed at equal volume as the E. coli mix. Overnight cultures of Lactobacillus crispatus CG-12 (10⁶ CFU/mL, 10 μl) were inoculated into 10 mL MRS broth and incubated anaerobically overnight at 37° C. The culture was centrifuged at 10,000×g for 5 min, and the supernatant was filtered by 0.22 mm filter to remove remaining cells. The inhibition volume of this supernatant against AR E. coli culture was tested in a series of modulated MRS media listed in Table 3. The media was modulated based on an assumption that 40% nutrient in the supernatant was depleted. Another set of 1×MRS media was modified in pH. The pH was identical to each supernatant-modified media. This set of media was used to evaluate the impact of pH on the inhibition activity.

TABLE 3 Modulated media used for growth inhibition test. Supernatant Supernatant 3× MRS 1× MRS Total % (mL) (mL) (mL) pH (mL) 0% — — — 6.42 5 5% 0.25 0.05 4.7 5.87 5 10% 0.5 0.1 4.4 5.49 5 20% 1 0.2 3.8 5.03 5 40% 2 0.4 2.6 4.58 5 50% 2.5 0.5 2 4.42 5

The Chicken Model.

All procedures were approved by the Institutional Animal Care and Use Committee (protocol No. 2012A00000061, The Ohio State University, Columbus, Ohio). Leghorn chicken were hatched and maintained at the Ohio Agricultural Research and Development Center (OARDC) poultry research teaching farm (two birds per cage with separate feed and water supply, controlled temperature, filtered air in the room and sterilized feed). Chicken fecal samples were collected on-site and examined for the presence of bla_(CMY-2) gene pools and microbial profile. Beginning on Day 5 post-hatch, chicken were inoculated with a bla_(CMY-2) ⁺ E. coli cocktail (0.2 mL/bird, 10⁶ CFU/mL) every 24 hours for 4 consecutive days via gavage feeding using 20ga×1.5 inch animal feeding needle (Fine Science Tools, Foster City, Calif., USA). Chickens in non-inoculated control groups were fed with 0.2 mL of saline by the same method. Chickens were then set in cages for 11 days before antibiotic treatment, allowing the microbiota to stabilize.

Lactobacillus crispatus and Antibiotic Administration.

Lactobacillus crispatus CG-12 was susceptible to ampicillin. To monitor the impact of CG-12 on AR profiles during common ampicillin administration practice, low veterinary Amp dosages (30 mg/kg body weight per day) were selected instead of 300 mg/kg/day. Lactobacillus crispatus CG-12 was administrated in three periods: 1) Day 2 to Day 4 post-hatch; 2) throughout the stabilization; and 3) post-antibiotic challenge on Day 25 to Day 28. During these periods, chickens were inoculated with a Lactobacillus crispatus CG-12 suspension (0.2 mL/bird, 10⁶ CFU/mL) every 24 hours for 4 consecutive days via gavage feeding using 20ga×1.5 inch animal feeding needle (Fine Science Tools, Foster City, Calif., USA). Chickens were grouped and treated as shown in Table 4. Each group contained at least 6 chickens.

TABLE 4 Leghorn chicken groups subjected to inoculation and antibiotic administration treatments. Pre-AR Pre- Pre-AR inoculation bla_(CMY-2)+ antibiotic Amp inoculation L. crispatus E. coli L. crispatus (30 L. crispatus Group inocula inocula inocula mg/kg) inocula Lc-Saline + + — — — Saline- — + — — — saline Lc-Amp — + + + — Saline- — + — + — Amp Amp-Lc — + — + + Amp- — + — + — Saline — : saline administered at same column. LC: Lactobacillus crispatus CG-12. Amp: ampicillin.

Sample Collection.

Fresh feces were collected from each chicken on-site in the rearing facility. Fecal samples were collected at the 1^(st) and last day of Lactobacillus inoculation, once a day during the antibiotic administration period, and once every three days during antibiotic withdrawal period up to 14 days from initial antibiotic exposure.

DNA Extraction.

Total DNA from chicken fecal samples for real-time quantitative PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE) analyses were extracted according to a published method (Yu and Morrison 2004).

Real-Time Quantitative PCR.

TaqMan real-time PCR protocol was used to assess bla_(CMY-2) and 16 S rRNA gene pools in total DNA extracted from chicken fecal samples, as described previously (Zhang et al., 2013). The sequences of the primers were 5′-GCCGTTGATGATCGAATC-3′ (SEQ ID NO: 7) and 5′-GCGTATTGGCGATATGTAC-3′ (SEQ ID NO: 8), with bla_(CMY-2) probe 5′-6FAM AGTTCAGCATCTCCCAGCCTAATCC-BHQ1-3′ (SEQ ID NO: 9) (Zhang et al., 2013). The primers were synthesized by Sigma-Aldrich (St. Louis, Mo., USA), and the probe was synthesized by Biosearch Technology Inc. (Novato, Calif., USA). Each sample was assessed and analyzed in duplicates on a CFX96 system (Bio-Rad, Hercules, Calif., USA).

DGGE Analysis.

The 16 S rRNA V3 region was used for amplification of partial 16 S rRNA gene following a published procedure (Muyzer et al., 1993). The sequences of PCR primers used were 16 S-357F-GC and 16 S-518R; products were loaded on to an 8% acrylamide gel with a urea gradient from 40% to 60%. Electrophoresis was performed at 60° C., 83 V for 16 h using the Dcode system for DGGE (Bio-Rad, Hercules, Calif., USA). The finishing gel was stained with 0.01% ethidium bromide and imaged under ChemiDoc XRS system (Bio-Rad, Hercules, Calif., USA).

For analysis of the impact of Lactobacillus crispatus CG-12 on AR establishment (Day 5) and bla_(CMY-2) ⁺ colonization in GI microbiota (Day 9), and fecal DNA of 6 chickens from Saline-Saline group (SS1-SS6), 4 chickens from the Lc-Saline group (LS1-LS4) and 1 control subject (C) at Day 5 post-hatch were used as the template to amplify the 16 S rRNA gene V3 region.

To analyze the predominant bacterial population in GI microbiota after antibiotic administration, chickens orally administered 30 mg/kg body weight/day Amp were used as the template to amplify the 16 S rRNA gene V3 region. The fecal DNA of 4 chickens from Lc-Amp group (LA1-LA4), 4 chickens from Saline-Amp group (SA1-5A4) were used as templates to amplify the 16 S rRNA gene V3 region.

16 S Metagenomic Analysis.

For microbiota analysis, three chickens were randomly selected from group Amp-Lc and Amp-Saline. Fecal DNA of Day 25 and Day 28 from each chicken was subjected to analysis. The V3/V4 portion of the 16 S rRNA gene of the subjects were amplified by PCR following the standard protocol of 16 S Metagenomic Sequencing Library Preparation (Illumina support, 2013), and the products were sequenced on an Illumina Miseq sequencer at OARDC Molecular and Cellular Image Center. Paired-end joining and quality filtering were performed with Qiime (Caporaso et al., 2010). Only sequences longer than 450 bp with Phred quality score higher than 19 were used for phylotype analysis. Operational Taxonomic Units (OTUs) were picked using an open-reference OTU picking process with 97% sequence similarity. 10% of the sequences that failed to hit the reference database were subjected to de novo clustering. Other quality control perimeters were set as default. Phylogenetic analysis and taxonomic assignments of the V3 and V4 portion of the 16 S rRNA gene were made using Greengenes database (version 13_8). Additional phylotype comparisons and analysis were performed with the QIIME diversity analyses module.

Statistics.

One-way ANOVA analysis of the population size of AR gene pools was performed in SAS (version 9.4), to compare difference between the three batches of chickens. Significance was declared at P<0.05.

Results

Growth Inhibition Assessments.

The supernatant of Lactobacillus crispatus CG-12 formed inhibition zones with 8-9 mm in diameters on all E. coli plates, while no inhibition zone of E. coli supernatant was observed on cultured plates of Lactobacillus crispatus CG-12 (Table 5).

TABLE 5 The growth of bla_(CMY-2) ⁺ E. coli (CFU/mL) in modulated MRS media. % Log₁₀ Supernatant pH CFU/mL (CFU/mL) Control 0 6.4 6.7 × 10⁸ 8.8 20% Supernatant 20 5.3 5.7 × 10⁵ 5.8 pH 5.3 0 5.3 2.7 × 10⁶ 6.4 40% Supernatant 40 4.6 <10 <1 pH 4.6 0 4.6 7.8 × 10² 2.9 50% Supernatant 50 4.4 <10 <1 pH 4.4 0 4.4 <10 <1 CFU: colony forming unit

In the 0% supernatant-modified media, the overnight culture of E. coli had a total count of 8.8 log₁₀ CFU/mL. The 20% supernatant supplement reduced the E. coli count by 3 logs, ending with 5.8 log₁₀ CFU/mL. The corresponding 1×MRS (pH 5.0) had 6.4 log₁₀ CFU/mL of E. coli. With 40% supernatant, less than 1 log₁₀ CFU/mL was detected in the supernatant-modified media, while 2.9 log₁₀ CFU/mL was observed in the corresponding pH-modified media.

Early Colonization of Lactobacillus Crispatus and Reduced AR Gene Pool in GI Tract of Chickens.

Six chickens from the Saline-Saline group, four chickens from the Lc-Saline group and one free of any treatment were randomly picked to study the constitution of gut microbiota. DGGE analysis showed Lactobacillus crispatus was among the most predominant populations at Day 5 post-hatch, regardless of Lactobacillus crispatus CG-12 inocula (FIG. 1).

The bla_(CMY-2) gene pool and 16 S rRNA pool were analyzed via qPCR. Seven chickens from the Saline-saline group and eight from the Lc-Saline group were subjected to assessment. The ratio of bla_(CMY-2) copies to 16 S rRNA copies was calculated [(bla_(CMY-2)/16 S) %] to show the prevalence of bla_(CMY-2) in the total bacterial load. In the Saline-Saline group, 6 out of 7 chickens had a (bla_(CMY-2)/16 S) % ratio larger than 0.77, with only one exception (0.12). There were two subjects in this group that had an extremely high prevalence of the bla_(CMY-2) gene, accounting for 7.14% and 54.96% of the total 16 S copies. In the Lc-Saline groups, however, the (bla_(CMY-2)/16 S) % ratio was generally low in all subjects: A (bla_(CMY-2)/16 S) % ratio lower than 0.20 was detected in 7 out of 8 subjects; the highest one was 0.55, which was still lower than the average ratio in the Saline-Saline group.

Insignificant Inhibition of the Colonization of Bla_(CMY-2) ⁺ Marker Strains.

In the preliminary study, six chickens from the Saline-Saline group, four chickens from the Lc-Saline group and one free of any treatment were randomly picked to study the constitution of gut microbiota on Day 9, right after inoculation with bla_(CMY-2) ⁺ E. coli. DGGE analysis showed the Lactobacillus crispatus population was better maintained in the Lc-Saline group, but colonization of bla_(CMY-2) ⁺ E. coli was not affected by pre-inoculation with the Lactobacillus strain (FIG. 2). The AR gene pool increased from 8.8±0.3 log₁₀ (gene copies/g) to 9.9±0.6 log₁₀ (gene copies/g) in the Saline-Saline group, and from 8.2±0.2 log₁₀ (gene copies/g) to 9.8±1.0 log₁₀ (gene copies/g) in the Lc-Saline group. Overall, the bla_(CMY-2) gene pool had about a 1 log increase from Day 5 to Day 9 regardless of inoculation with bla_(CMY-2) ⁺ E. coli, and the E. coli inocula did not significantly increase its prevalence in gut microbiota.

Insignificant Reduction of AR Gene Pool During Antibiotic Treatment.

Four chickens from the Saline-Amp group and eight from the Lc-Amp group were subjected to assessment of the bla_(CMY-2) and 16 S rRNA gene pool, to show the prevalence of the bla_(CMY-2) gene on Day 21 (during treatment) and Day 25 (after treatment). A large prevalence of bla_(CMY-2) gene pool was detected in both groups on Day 21: bla_(CMY-2) and 16 S rRNA gene pool was 8.7±0.8 log₁₀ (gene copies/g) and 8.5±0.7 log₁₀ (gene copies/g) in the Saline-Amp group. In the Lc-Amp group, bla_(CMY-2) and 16 S rRNA gene pool was 10.0±1.0 log₁₀ (gene copies/g) and 9.2±1.07 log₁₀ (gene copies/g). On Day 25, the bla_(CMY-2) and 16 S rRNA gene pools were 9.8±0.9 log₁₀ (gene copies/g) and 10.5±1.0 log₁₀ (gene copies/g), respectively the in Saline-Amp group; while in the Lc-Amp group, the bla_(CMY-2) and 16 S rRNA gene pools were 9.2±0.9 log₁₀ (gene copies/g) and 10.4±0.8 log₁₀ (gene copies/g), respectively. The overall prevalence of bla_(CMY-2) decreased from Day 21 to Day 25, but no significant difference was observed between these two treatment groups.

The predominance of the bla_(CMY-2) ⁺ E. coli marker was not reduced by pre-antibiotic inoculation with Lactobacillus crispatus CG-12 (FIG. 3A-3C). The selective enrichment of E. coli on Day 21 was more significant in the Lc-Amp group (FIG. 3B).

A possible explanation for these results is that because Lactobacillus crispatus CG-12 was susceptible to Amp, this strain may have been selectively eliminated during antibiotic treatment and therefore made no contribution in the treatment groups.

The post-antibiotic change of microbiota constitution. Three randomly selected chickens from the Amp-Lc and the Amp-Saline groups were subjected to 16 S rRNA phylotyping analysis to illustrate the impact of post-antibiotic inoculation of Lactobacillus crispatus CG-12 (FIG. 4).

Discussion and Conclusion

The bacteria competition test showed that Lactobacillus crispatus CG-12 has good in vitro inhibition capabilities against bla_(CMY-2) ⁺ E. coli. Inhibition was largely due to the ability of CG-12 to produce lactic acid and reduce the pH, as media modified to have the same pH exhibited similar growth inhibition. Except for lactic acid, Lactobacillus crispatus CG-12 may also produce other inhibitory substances which contribute to the reduction of E. coli in 20% and 40% supernatant-modified media compared to corresponding pH-modified media.

The in vivo colonization of Lactobacillus crispatus CG-12 against bla_(CMY-2) ⁺ E. coli was further evaluated in poultry GI microbiota. Lactobacillus crispatus CG-12 is a commensal bacterial species isolated from chicken GI microbiota, which has good colonization fitness in chicken gut. Analysis of the constitution of GI microbiota on Day 5 shown that Lactobacillus crispatus was the predominate population at early chicken growth stages, in agreement with previous isolate-based research (Lu et al., 2003). The predominance implied a favored environment for Lactobacillus crispatus in chicken GI tracts at this stage of growth. The decrease in the bla_(CMY-2) gene pool indicated successful colonization of bla_(CMY-2) Lactobacillus crispatus CG-12 in the GI microbiota. It is possible that well-colonized bla_(CMY-2) Lactobacillus crispatus CG-12 compete with homogeneous and heterogeneous bacteria and contribute to a reduction of AR bacteria and AR genes.

Lactobacillus crispatus lost its prevalence during chicken maturation, and other Lactobacillus and Firmicutes population become dominant during the natural transition of GI microbiota (Lu et al., 2003). The ineffectiveness of Lactobacillus crispatus CG-12 to reduce the AR gene pool and AR bacteria during Weeks 2-3 may be due to loss of predominance in the GI microbiota. As Lactobacillus crispatus CG-12 was susceptible to ampicillin, it was also likely selectively eliminated by antibiotic treatments in Week 4. Furthermore, the targeted AR bacterial E. coli strains were distantly related to Lactobacillus crispatus CG-12. The E. coli strains may locate in distant niches in the gut, making it more difficult for Lactobacillus crispatus CG-12 to eliminate. Early studies on displacement of indigenous AR E. coli were achieved by using susceptible strains from the same species (Linton et al., 1978). Future trials to use commensal or probiotic stains for clonal decontamination should take into consideration the ecological position of the targeted strains.

The constitution of GI microbiota recovered fast once the antibiotic selective pressure was removed. The dominance of Firmicutes recovered within three days without any intervention. Inoculation of Lactobacillus crispatus CG-12 did not accelerate recovery; rather the prevalence of Proteobacteria was even higher in the inoculated group.

In conclusion, inoculation of Lactobacillus crispatus CG-12 is a promising strategy to reduce early colonization of AR in chicken GI microbiota.

Example 3

Competition Test Against Resistant Escherichia coli Strains

Four previously identified Amp^(r) (ESBL) Escherichia coli strains were introduced to the study to serve as antibiotic resistant bacteria marker, including strain M9-1 (CA-1 previously), M9-4 (CA-4), M9-12 (CA-20) and 933-36, all were previously recovered from poultry, identified with high MIC (>256 μg/mL) and were found to grow well in MRS broth. The competence of probiotic strains against these Amp^(r) Escherichia coli strains was examined with the following set up, 1) a quantity of 10⁵ cells from one probiotic strain is inoculated with 10⁵ or 10⁶ cells of one Amp^(r) Escherichia coli strain (ratio of 1:1 and 1:10) in MRS broth and then incubated at 37° C. for 24 hours. The culture was then recovered and inoculated on MRS agar supplemented with 32 μg/mL ampicillin and then incubated anaerobically at 37° C. for 48 hours. The growth performance of isolates on the agar was recorded. A complete inhibition is defined as absolutely no growth on the MRS agar supplemented with ampicillin (designated as “I”). A partial inhibition is defined as attenuated growth of Amp^(r) Escherichia coli strain on the MRS agar (designated as “P”). No inhibition is defined as complete growth of Amp^(r) Escherichia coli strain on the MRS agar (designated as “N”). The competition test result is included in Table 6.

TABLE 6 Competition test between probiotic strains and Amp^(r) (ESBL) Escherichia coli strains M9-1(CA-1) M9-4 (CA-4) M9-12(CA-20) 933-36 1:1 1:10 1:1 1:10 1:1 1:10 1:1 1:10 1-1  P N N N N N/A N N 1-3  P N N N N N/A N N 1-9  P N N N N N/A N N 1-14 I, c I, c I, c I, c I, s N/A I, s I, c 1-22 N N P N N N/A N N 1-31 P N I, s I, s I, s N/A I, s N 1-35 P N P N N N/A N N 2-2  I, c N I, c I, s I, c N/A I, c N 2-26 P N P N N N/A N N

In addition, some inhibition effect can be divided as bacteriostatic effect (designated with “s”) and bactericidal effect (designated with “c”), with bacteriostatic effect defined as significant recovery of Amp^(r) Escherichia coli strain on MRS agar supplemented with ampicillin after a week of shelf storage; while bactericidal effect defined as no recovery of Amp^(r) Escherichia coli strain under the same conditions.

In summary, besides CG-12 (now designated as WZ-12), three more LAB strains, 1-14, 1-31, and 2-2, especially exhibited a broad spectrum inhibition to the multidrug resistant E. coli strains tested.

Example 4 Genome Sequencing of Isolates.

In addition to CG-12 (now designated as WZ-12), 16 S rRNA sequencing further identified three probiotic strains. Two of strains were Lactobacillus salivarius (1-14) and Lactobacillus reuteri (2-2). The third strain turned out to be Streptococcus alactolyticus. Previous literatures illustrated the application of Lactobacillus salivarius CTC2197, as well as certain strains of Lb. reuteri and Streptococcus alactolyticus as probiotics to inhibit certain foodborne pathogens in poultry, and mostly in swine.

To further validate the novelty of our isolates, two of the Lactobacillus strains were further subjected to full genome sequencing for genetic identification to clear up the background for potential patenting as backup strains for CG-12 (WZ-12). The genome accession numbers for the three probiotic strains used in this study include: OSU_LbSa1.14″, accession number QOZV00000000; “OSU_LbReu_2.2_v1”, accession number QOWD00000000; and WZ-12 (previously CG-12, 721-12), accession number QKVQ00000000.

Animal Studies.

The probiotics as disclosed herein were applied to chickens raised in a poultry facility, with the aim to examine the effectiveness of the treatment phenotypically and genetically (fecal microbiota) and physiologically (chickens); and to adjust receipt and procedure of feeding if necessary.

Treatments Effective in Modulating Gut Microbiota.

The metagenomics assessment #1 (FIGS. 5A and B) illustrated bacterial population in pooled feces of chickens treated with ESBL E. coli with or without probiotic protection, without antibiotic applications. The results suggested that without any inoculation, proteobacteria (gram-negative bacteria including E. coli etc.), Cynobacteria and Firmicutes were the dominant population (FIG. 5A, Lane 2). Feeding probiotics cocktail (Lb. crispatus WZ12, Lb. salivarius 1-14 and Lb. reuteri 2-2) made Firmicutes (the phylum including Bacilli, Clostridia etc., such as Lactobacillus) the absolute dominant population in fecal microbiota (FIG. 5A, Lane 1), significantly reduced Proteobacteria (including previously inoculated E. coli) in the poultry fecal/gut microbiota. Inoculating Lactobacillus probiotic cocktail before exposure to ESBL E. coli also reduced the amount of (colonization of) Proteobacteria in fecal microbiota (Lane 3). Lb. crispatus CG 12 (renamed to WZ12) also was effective in reducing previously inoculated E. coli and made Firmicutes the dominant population (Lane 4). Probiotic cocktail given after E. coli exposure was also effective in reducing the previously colonized E. coli population (Lane 5). Tween 80 treatment assisted the colonization of Proteobacteria but not the Firmicutes. So in summary, the inoculation of the Lactobacillus probiotics significantly helped with preventing and reducing Proteobacteria.

It was recognized that even if antibiotic resistant bacteria may be reduced by probiotic treatment, some of those resistant bacteria seeds might still retain in the microbiota, and could pop up again when exposed to antibiotics. Therefore in another set of the experiment, following probiotic and ESBL E. coli exposure, the chickens were further treated with Amp by oral or muscle injection. As illustrated in FIG. 7, ESBL E. coli seed dominated the fecal microbiota after oral Amp treatment. But Probiotic treated chickens (Group 1 &2) retained more Firmicutes or Cynobacteria than chickens without probiotic treatment (Group 3 with inoculated ESBL E. coli & Group 4 natural flora, with one outlier). Despite Firmicutes or Cynobacteria were still a minor population in Group 1 & 2 compared to Proteobacteria, the saved diversify seeds enable better recovery once the antibiotic selective pressure was removed. Furthermore, changing antibiotic administration from oral to injection made significant difference in retaining Firmicutes with (Group 7) or without ESBL E. coli inoculation (Group 5).

In conclusion, by changing antibiotic treatment from oral to injection, feeding probiotics and manipulating ways of probiotic administration, ESBL E. coli can be significantly reduced in fecal microbiota and protect gut microbiota diversity in poultry.

Example 5

The Impact of Ampicillin Administration Routes and Inoculation of Amp^(r) E. coli on Poultry Gut Microbiota.

FIG. 7A-B illustrates the impact of ampicillin application on gut microbiota of chickens. The data illustrated that without antibiotic application (FIG. 7A), Lactobacillus dominant, E. coli/Shegilla insignificant. Without inoculation of the “bully” E. coli M 9-4 cocktail, given ampicillin by muscle injection led to minimal changes (FIG. 7B), but by oral ampicillin led to decrease of Firmicutes (still dominant) and significant increase of Proteobacteria, but within Proteobacteria only small amount due to E. coli/Shegilla, mostly due to Klebsiella (FIG. 7C). In chickens inoculated with the “bully” E. coli cocktail, if Amp was given by muscle injection, Firmicutes still dominant but with which Lactobacillus drastically reduced, and Clostridium et al. quickly increased (FIG. 7D); if Amp was given by oral feeding, then Firmicutes changed from dominant to minority, and Proteobacteria, within which E. coli/Shegilla became dominant (FIG. 7E). The results clearly illustrated the major impact on oral ampicillin administration on poultry gut microbiota by diminishing Lactobacillus, increasing Clostridium, and massively increase Firmicutes due to Amp^(r) E. coli in inoculated chickens and Klebsiella in non-inoculated chickens.

The Impact of Lactobacillus/Streptococcus Probiotic Cocktail Feeding Study on Mice Gut Microbiota.

In mice inoculated with Amp^(r) E. coli and Tet^(r) Enterococcus cocktail for 4 days followed by normal food and gavage saline, the Amp^(r) population on LB plates, presumably being Amp^(r) E. coli, were 82% (mouse 4R) and 90% (mouse 4N). If with Amp^(r) E. coli and Tet^(r) Enterococcus cocktail for 4 days followed by normal food and gavage feeding of probiotic cocktail instead of saline, the Amp^(r) population on LB plates, presumably being Amp^(r) E. coli, were 78% (Mouse 6L), 58% (6R) and 92% (6N). The 58% Amp^(r) E. coli was the lowest detected so far, which strongly suggested the potential functionality of the probiotic cocktail in reducing the Amp^(r) E. coli subpopulation. Still pending for the metagenomic fecal microbiota profiling data.

Molecular Mechanism in the Persistent “Bully” Amp^(r) E. coli Strains.

Plasmid extraction showed that the poultry oriented Amp^(r) E. coli strains used in inoculation carry at least 3 plasmids. The Amp^(r) phenotype was persistent even when the strains were cultivated in LB broth without ampicillin for many generations. Electroporation study and DNA sequencing data confirmed that the Amp^(r) is encoded by a large plasmid, but the plasmid was stably retained in the host event with the corresponding antibiotic selective pressure. In a competition study, DH5α failed to overcome the “bully” Amp^(r) E. coli strain. When the “bully” strain M9-4 was inoculated on the LB plate covered with DH5a, it showed clear inhibition zone for all three dilutions (FIG. 8A). The data illustrated that strain M9-4 is “bully” also because it carried mechanism to over-compete the other E. coli strains.

Second Group of E. coli Probiotic Derivatives to Combat the “Bully” Strains.

By manipulating the DH5α with genetic elements, multiple DH5α derivatives M9-4-1 were received that are no longer inhibited (clear inhibition zone) by the “bully” strain M9-4 but with white growth ring (FIG. 8A-B). These new E. coli strains and derivatives can serve as the second group of probiotics, to be used in combination of the Lactobacillus/Streptococcus probiotics, to further over-compete towards eliminating the “bully” ESBL strains in food animal production.

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Publications cited herein are hereby specifically incorporated by reference in their entireties and at least for the material for which they are cited.

It should be understood that while the present disclosure has been provided in detail with respect to certain illustrative and specific aspects thereof, it should not be considered limited to such, as numerous modifications are possible without departing from the broad spirit and scope of the present disclosure as defined in the appended claims. It is, therefore, intended that the appended claims cover all such equivalent variations as fall within the true spirit and scope of the invention.

SEQUENCES Partial sequence of pM9-4 A (biggest plasmid) Large fragment by sequence walking SEQ ID NO: 10 CCTCTCCCCCCACACAACGCCACCTCCCGTCAGCACAACATGTGGTGC CGGATTCAGCTGCTGATAACACTATATGTTGTGTCATCTCCCTGACCT GTGATGCGTCGCGCAGGGGCGGAAAACAGCGATATGATGATTTCCTCA GCGTGGTACACTTCCGGAAAGTTATGAATAGGAAAAAAATCGGATCTG CCTGAAATGGGCATCCAGTAATTTAATAGCGTGGTTATATGCCTGCTT ATTATCTGACAGGTGATGATTTATTTAGGGGAAAATAATTCATGCTGA CAGAGTGTTGTGTTGCCATGCGTAATAACTCTGAGCGACTGTTGCTTC CGGTATCAGTTGAGTGAGGATTTTCAGACCACCACGTTTTACTGACCA GTAAAAATTTTTTTTGCCCGCAAGGCTGACAAGTGACTTCTTTTAGGG AAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGC CATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGT GAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC CGCATGGAGCAGATTCTGCCATGGCAAAACATGGTGGAAGTCATCGAG CCGTTTTACCCCAAGGCTGGTAATGGCCGGCGACCTTATCCGCTGGAA ACCATGCTACGCATTCACTGCATGCAGCATTGGTACAACCTGAGCGAT GGCGCGATGGAAGATGCTCTGTACGAAATCGCCTCCATGCGTCTGTTT GCCCGGTTATCCCTGGATAGCGCCTTGCCGGACCGCACCACCATCATG AATTTCCGCCACCTGCTGGAGCAGCATCAACTGGCCCGCCAATTGTTC AAGACCATCAATCGCTGGCTGGCCGAAGCAGGCGTCATGATGACTCAA GGCACCTTGGTCGATGCCACCATCATTGAGGCACCCAGCTCGACCAAG AACAAAGAGCAGCAACGCGATCCGGAGATGCATCAGACCAAGAAAGGC AATCAGTGGCACTTTGGCATGAAGGCCCACATTGGTGTCGATGCCAAG AGTGGCCTGACCCACAGCCTAGTCACCACCGCGGCCAACGAGCATGAC CTCAATCAGCTGGGTAATCTGCTGCATGGAGAGGAGCAATTTGTCTCA GCCGATGCCGGCTACCAAGGGGCGCCACAGCGCGAGGAGCTGGCCGAG GTGGATGTGGACTGGCTGATCGCCGAGCGCCCCGGCAAGGTAAGAACC TTGAAACAGCATCCACGCAAGAACAAAACGGCCATCAACATCGAATAC ATGAAAGCCAGCATCCGGGCCAGGGTGGAGCACCCATTTCGCATCATC AAGCGACAGTTCGGCTTCGTGAAAGCCAGATACAAGGGGTTGCTGAAA AACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGG GCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGG ATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGG CATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACT GAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCTTAAGTA TCATTGCAGCAAAGATGAAATCAATGATTTATCAAAAATGATTGAAAG GTGGTTGTAAATAATGTTACAATGTGTGAGAAGCAGTCTAAATTCTTC GTGAAATAGTGATTTTTGAAGCTAATAAAAAACACACGTGGAATTTAG GAAAAACTTATATCTGCTGCTAAATTTAACCGTTTGTCAACACGGTGC AAATCAAACACACTGATTGCGTCTGACGGGCCCGGACACCTTTTTGCT TTTAATTACGGAACTGATTTCATGATGAAAAAATCGTTATGCTGCGCT CTGCTGCTGACAGCCTCTTTCTCCACATTTGCTGCCGCAAAAACAGAA CAACAGATTGCCGATATCGTTAATCGCACCATCACCCCGTTGATGCAG GAGCAGGCTATTCCGGGTATGGCCGTTGCCGTTATCTACCAGGGAAAA CCCTATTATTTCACCTGGGGTAAAGCCGATATCGCCAATAACCACCCA GTCACGCAGCAAACGCTGTTTGAGCTAGGATCGGTTAGTAAGACGTTT AACGGCGTGTTGGGCGGCGATGCTATCGCCCGCGGCGAAATTAAGCTC AGCGATCCGGTCACGAAATACTGGCCAGAACTGACAGGCAAACAGTGG CAGGGTATCCGCCTGCTGCACTTAGCCACCTATACGGCAGGCGGCCTA CCGCTGCAGATCCCCGATGACGTTAGGGATAAAGCCGCATTACTGCAT TTTTATCAAAACTGGCAGCCGCAATGGACTCCGGGCGCTAAGCGACTT TACGCTAACTCCAGCATTGGTCTGTTTGGCGCGCTGGCGGTGAAACCC TCAGGAATGAGTTACGAAGAGGCAATGACCAGACGCGTCCTGCAACCA TTAAAACTGGCGCATACCTGGATTACGGTTCCGCAGAACGAACAAAAA GATTATGCCTGGGGCTATCGCGAAGGGAAGCCCGTACACGTTTCTCCG GGACAACTTGACGCCGAAGCCTATGGCGTGAAATCCAGCGTTATTGAT ATGGCCCGCTGGGTTCAGGCCAACATGGATGCCAGCCACGTTCAGGAG AAAACGCTCCAGCAGGGCATTGCGCTTGCGCAGTCTCGCTACTGGCGT ATTGGCGATATGTACCAGGGATTAGGCTGGGAGATGCTGAACTGGCCG CTGAAAGCTGATTCGATCATCAACGGCAGCGACAGCAAAGTGGCATTG GCAGCGCTTCCCGCCGTTGAGGTAAACCCGCCCGCCCCCGCAGTGAAA GCCTCATGGGTGCATAAAACGGGCTCCACTGGTGGATTTGGCAGCTAC GTAGCCTTCGTTCCAGAAAAAAACCTTGGCATCGTGATGCTGGCAAAC AAAAGCTATCCTAACCCTGTCCGTGTCGAGGCGGCCTGGCGCATTCTT GAAAAGCTGCAATAACTGACGATGAGGCCCAGGATATTGGGCCTCCTT TCTTTCTCTTTTTTTCCTGTTGTCATCTACACTTAACAAAAATACAGC AAGGAAAATCCCATGCGCATTTTGCCCGTCGTTGCTGCAGTTACGGCT GCATTCCTGGTTGTCGCGTGTAGCTCCCCGACACCGCCGAAAGGCGTT ACCGTGGTAAATAACTTTGATGCCAAACGCTATCTGGGAACCTGGTAT GAAATTGCGCGCTTCGACCATCGTTTCGAGCGCGGATTGGATAAAGTG ACCGCAACATACAGCTTGCGCGACGACGGCGGCATCAACGTTATTAAC AAGGGCTATAACCCTGACAGGGAGATGTGGCAGAAAACGGAAGGGAAA GCCTATTTCACCGGCGACCCAAGCAGAGCCGCGCTTAAGGTTTCTTTT TTCGGCCCCTTCTATGGCGGGTATAACGTAATTGCACTCGACCGGGAA TATCGTCACGCGCTGGTTTGTGGTCCGGATCGCGACTACCTGTGGATC CTTTCACGGACCCCTACTATTTCAGATGAAATGAAACAGCAAATGTTA GCCATCGCGACCCGGGAAGGGTTTGAAGTGAATAAACTGATTTGGGTG AAACAGCCTGGCGCTTAGTGAGTGCTCAGCTTCAGACCAATAATGCCA GCAACGATCAGCCCAAGGCTCAGCAAACGTGCCGGGCTGGCAGACTCA CCCAGCAGCAAAATCCCTGTAATGGCCGCCCCAACAGCGCCAATACCG GTCCAGACCGCATAAGCGGTTCCTACAGGCAACGTGCGCATTGCCCAA GAGAGCATGGCGATACTGACGATCATCGCCGCAATAGTGATAATGCTT GGCGTAAGACGCGTAAAACCGTGGGTGTATTTCAGGCCAATCGCCCAG ACAACTTCGAGCAAACCTGCAATTAATAAAACGATCCAGGACATATCA GGCTCCAGAACAATGGGGCCGTCCCCGGTGAAAGAAGCGTTTGCAGGT CGTCCTGCAAAGCTAATGTGTGAAATGGCATTTTTGCCCGGAAGAAAA TGAATTTCAACCTTTTTATTCACCGCCTGCTAAAAGCAAGAATTAAGC ATAATTAGCGGCGTAGTTCCCGCATTATTACCGGAAATCGATTATTCC CCGGTATCTGGTAACTGGCGCTCCCTTCCTTCTGGCCTGATGTATAGG CTCAGCGAACTCTCTGTTCTCAGCTACGAAGCTGTCGTGTGTGTAGAT AATGTGTTTGTTGAAGATACTCCTTATGGTGGAGCGGGTGAATATAGT TTGCATAAAAACGCAGCTATGTTGGGAGTAAAAGCACTGCGGTTATCA CGAGAACTGAGAATGTTATGTGGCCTCCCTCTGCACGGCCTTTCCGAT ACACTATCGCCAACGAGGTTGGTATTGTTGAAAGCCAGAGGTAAAACA CTCCAAAAGGAGTACGAAATGGTAAAGAAGTCTAAAAAGACCGAGCAA GAGATTGAGGATTTCATAAAGGGGACATCATGAGTGGTCCACAATTGC TTTCCCTGCCTGGTTCTTTTTTAACGCCTCCGGCAACATTACCTGTTG CCATTGATTACCCGGCTGCGCTGGCACTCCGCCAGATGTCGATGGTTC ATGATGAACTGCCAAAATACCTGCTGGCCCCTGAAGTGAGCGCCCTGC TCCATTACGTGCCGGATCTGCGCCGCAAAATGCTGCTGGCCACACTGT GGAACACCGGTGCGCGCATTAATGAAGCACTGGCGCTGACGCGGGGGG ATTTTTCGCTCACGCCTCCGTATCCGTTTGTGCAGCTGGCCACTCTGA AGCAGCGGACAGAAAAAGCCGCCAGGACGGCAGGAAGGATGCCCGCCG GTCAGCAGACTCACCGTCTGGTTCCGCTCTCCGACGCCTGGTACGTCA GCCAGCTGCAGACGATGGTGGCCACACTGAAAATCCCCATGGAACGGC GTAATAAACGAACAGGCAGGACAGAGAAAGCGCGGATCTGGGAAGTGA CGGACAGAACGGTCAGGACCTGGATTGGGGAGGCGGTTGCCGCCGCTG CCGCTGATGGTGTGACGTTCTCTGTCCCGGTCACGCCACATACGTTCC GCCATTCCTATGCGATGCATATGCTGTATGCCGGTATACCGCTGAAGG TCCTGCAGAGTCTGATGGGGCATAAGTCCATCATCTCAACGGAGTCTA CACAACGTGTTTGCACTGGATGTGGTTGCACGGCACCGGGTGCAGTTT TCGATGCCTGAGTCCGATGCGGTGTCTATGCTCAAAAGAATTCCATAA GCTCTGACTTTTTTAAATCCCTTTCGGATATCTCATGKATATATTATC GGTATTTCATATTCTGTTGACATGCAGGACCGGTATAGAGTAAAAAAA CATCTGTTGAGTACCTCTTGGATATCCGAAAGGTGTCTTATGGGGTCT TTMTGGRTATTACATGTGGATTCTGGAGATACACTATGCCTGTTATTG CTAATACGCATCCCAAAGGYGGTGTGGGTAASACAACTTCATCCRTAA ACATAGKTGGTGAAATGAAGTCTGATACAGTTGATCTGGATACTCATA CCGGGCTTTCTATCATTCTGGGGCTGAGACCTGATGGAAAAGAAATTT CCGTGAAAGTACCCAAAACAGAGGATGAGTTAATCGATATTATGACTC CCTACAAGAACAACCATAAGACGTTACTTATTGACTGTGGGGATTTGA CTTCATATCTTACCCGTACTGCGATTGCCTTTGCCGACTGAGTTATTG GCCCTTCAAAAGACTCCCTGACTGAACGTATTGTCTGATGCATTTGAT GGATACTGGACGAAATCGCTCTATCATGGGGACCGATMTAACTGCTCA CCTGTATCTCTGTAAAGTTAATCCTAACAAGAAGAAATTCCCTAAGCT TGATGCAATCCTGCCATCGTTCAAACATCTGAAGCTGATGAAGAGCCG CATTTCTGCTCGTGCAGAATTTGATGATGTCATTGAKACTGGRATGGG AATCACTGAGYCTGTTCATGGGCGCTATTCKGCAGGAGGTAAGGAAGT TATTGCCCTGATCGAAGAAATTAATCATCTGATTGAAAATMACAAACA GTAAGGTGTATCTATTGGGTATCCATATAGTATMCTTTGGGCTTTTAA TGGATATCTTTTARGTATCTAACAAACATCCTGGGTTAYCTCATGAGC AAAGCGAAATTT (1..6252) Nucleic acid sequence of pM9-4 A SEQ ID NO: 11 tagaatttcggcatccacaaccaatggcaggaagcccgatgcaaaaat ttttaaggagagctcttttaatgaaaattgctcagcaattactggagg ccgttctgcaatttatgaatgcatctgcaatgactcaggtgctgacgt tgatattcctggctctgataatacaggtactgaaaacattaattacgg cgtggatagtaagaaaaccatcttcaggagagatggttttagaccgga aacctgactctgccgggcgtaaggatcactgcaggcagctgtctcaac aaaggaaaaaacatggctgactggtttattgcaactgaaggtgtgaag gtggtgaaagatagtgccagcctgtggccgcagatcatcacggcggtt ttgtctgccggtactgcatttggtggtgtgtggtacgggcagtggcgg ataacacagcgagaggaggaagctgcaacagcgaagctggtcagcgaa cgtctctttattgccacggagctggtttttctgctggagaggtttgcg cagcgttgtgctccagcagcaacagcaactgtggagcacgatcaggat ggcagaggagaagctgagttcttattcctagattctacgtcagtactt caaaaagcataatcaaagccttgataaatatgcattccttcgaaattc agctttcacccattgggtgaaagaaaagtgctcaaaaatatgttaaat tatcagcttttatgactcgatatatggtaaaataatagtaagaaaagt agtaaaaaggggttctaattatgattaataaaattgatttcaaagcta agaatctaacatcaaatgcaggtctttttctgctccttgagaatgcaa aaagcaatgggatttttgattttattgaaaatgacctcgtatttgata atgactcaacaaataaaatcaagatgaatcatataaagaccatgctct gcggtcacttcattggcattgataagttagaacgtctaaagctacttc aaaatgatcccctcgtcaacgagtttgatatttccgtaaaagaacctg aaacagtgtcacggtttctaggaaacttcaacttcaagacaacccaaa tgtttagagacattaattttaaagtctttaaaaaactgctcactaaaa gtaaattgacatccattacgattgatattgatagtagtgtaattaacg tagaaggtcatcaagaaggtgcgtcaaaaggatataatcctaagaaac tgggaaaccgatgctacaatatccaatttgcattttgcgacgaattaa aagcatatgttaccggatttgtaagaagtggcaatacttacactgcaa acggtgctgcggaaatgatcaaagaaattgttgctaacatcaaatcag acgatttagaaattttatttcgaatggatagtggctactttgatgaaa aaattatcgaaacgatagaatctcttggatgcaaatatttaattaaag ccaaaagttattctacactcacctcacaagcaacgaattcatcaattg tattcgttaaaggagaagaaggtagagaaactacagaactgtatacaa aattagttaaatgggaaaaagacagaagatttgtcgtatctcgcgtac tgaaaccagaaaaagaaagagcacaattatcacttttagaaggttccg aatacgactactttttctttgtaacaaatactaccttgctttctgaaa aagtagttatatactatgaaaagcgtggtaatgctgaaaactatatca aagaagccaaatacgacatggcggtgggtcatctcttgctaaagtcat tttgggcgaatgaagccgtgtttcaaatgatgatgctttcatataacc tatttttgttgttcaagtttgattccttggactcttcagaatacagac agcaaataaagacctttcgtttgaagtatgtatttcttgcagcaaaaa taatcaaaaccgcaagatatgtaatcatgaagttgtcggaaaactatc cgtacaagggagtgtatgaaaaatgtctggtataataagaatatcatc aataaaattgagtgttgctctgtggataacttgcagagtttattaagg a (1..2113) Additional sequenced fragments from pM9-4A Colicin 1Forward SEQ ID NO: 12: TGACATTAACAAAAAAATTAATGCAAAAGATCGTGCAGCGATTGCCGC AGCCCTTGAGTCTGTGAAGCTGTCTGATATATCGTCTAATCTGAACAG ATTCAGTCGGGGACTGGGATATGCAGGAAAATTTACAAGTCTTGCTGA CTGGATCACTGAGTTTGGTAAGGCTGTCCGGACAGAGAACTGGCGTCC TCTTTTTGTTAAAACAGAAGCCATTATAGCAGGCAATGCCGCAACGGC TCTTGTTGCACTGGTCTTCAGTATTCTTACCGGAAGCGCTTTAGGCAT TATCGGGTATGGTTTACTGATGGCTGTCACCGGTGCGCTGATTGATGA ATCGCTTGTGGAAAAAGCGAATAAGTTCTGGGGTATTTAAATAAAATA TAAGACAGGCTGTCTATCTTACAGACAGCCTTTTTATAATAACAGAAA GAATATATATCATACTTAACGGAAGAGATAATATGAAAACAGTACCCG TATAAACAGCAAGCAATCCCATTTTCCCAGGTGTATCAGCAAAAAAAC CGCTGTTCCAGAAATCAGGCCGGGTAAATTTCAGAGCTGTATCTTCAA TATACCATTTTGCAACCGGATACAAAACCATTCCGCAGAGAGAAATAC ACCAGAACAGTAATCTGTATTTAAAATCATAATCCCATGACATATACA GCATATATCCCCCCGTCACCCATCCCCACCACATATTATTAAAATAAT ATTTTCTGTTCATCTGCCTGTTTTCCTTTCTTTTGCACTTTTGTCAGT GTACTGATGCATGACAACACAACCACAGCATGATAATAATAATCAATA ACAATAAGC (1..825) Colicin1 Reverse SEQ ID NO: 13 GCCTTGGCCGTTTACTCCTGTCGCTTATTGAAGATGCAGGGCTGAATA AACTGGATTCCCTGGCTAATCCCCGTATCCGGACTAATTATCGTGAGT GTCTTGATGCCATACGGCAGGTTACACTACAGCAGGAGTATATTCGGG GAAGAGCCTTATCTGAAATTATCCATTTCCGGCCAGGAATGTCTGAAA GGTCTCAGGAGCGGTTAATGGAAACGCTGGAGAATTCAGAACGACACT GGCCTGCCAGAAGAAAGCATATGTTCTTTCAGATTTTTATGGCGCAGC ACATCTGTCGTGATGCTGTGGAAATTCACTGGGCGAACGGTAATATTC AGGTCATCAGACCTGTGCGGGGGATCAGTATTAATGGTGAAGCGCAGG GCGGAATACGTCCCCCTTACTGGGTTATTCTTGCTTTTTGCCGGAGTG CCGATGGCAGAATCATCTGCAGTGAAGGGTATGCTCATGCTCTTTATC AACTGACATGTCCGGTGCCTGTGGACAGCAAACTGGAACGAAACACGC TCACTGCTCTTCTGAATGTGGCCAGCTGGCTTAAAAGAAAGCCAGGTA CGCCGGAATTAAGTCTGGAAAGGCCCCTGTTTGATACAGAAGTTTATG TTAATGGTGAAAAGAAATATGTACTGCCGGATTTCATTGTCACAGCAA GGGCTCCTGACGGAAAGACGGCCAGAGTGGTCATCGAAACGATGGGAT ATGAAGACAGTGATTACTGCGCGAGAAAATCCAGGCAGCATACCGGCA TGAAGCAGATTGGTGTTCTGCATACCGATCCACCGAAATGGCTGGATA ACGATCATCCCCCTTTTAAGAAACATATGTACGGTGTTTTTATGCATC TCAGGTACTGAGATATTTTGTGGCTCAGTTCTGTAACTTTTCCCGTAA CATTGTCTGTTGTTACGGGAAAGTCCGGTTTTTGTATTGCACCAGAGA ATACCCAGACTGTGATGCTGCCACAGCGTCAGCAGGCTTTCTGAACGG TGTAACATCACTTCATGTTAATGATAATCACTATCATCAAATCTTGAC ATGCCATTTTCTCCTTAATAAATTAATACTGTATATGTATCCATATGC GTAAGCAGTTAATTCATTTGTTTTCCTCAGAGGATGAAGGAGATACCG AATGTCTGACCCTGTACGTATTACAAATCCCGGTGCAGAATCGCTGGG GTATGATTCAGA (1..1212) IS2001 Forward SEQ ID NO: 14 GAAGCCTCGCCCGACAGGGCGGGGAGCAGTCACGGGTGGTCTGGAGGT CATGCGGCGTGTCCTCTGCACTCGCCGGAATAAGGAAGTCGCCGGCGG CTCCGCTTTTACCCGGCCATGCGGGGCATGGCCTTGTGGGTTTTCAGC TCTGTGGCCTCAGCGTCGTGTGCGGGCTGTGCCGTGCCTCCA (1..186) IS2002 Reverse SEQ ID NO: 15 TGGTGCGGGCGTTTTCCATCACTGTCATCATTTGACCGGTTTTTCTGG CAGGAGGAACCACTCTGGCGGCTGATTTTTGAAGCCGGTGAGGCCGGT CGTGGTGCACCGGTACAGATACGTGCACTTGAGCAGTGGATGATCCCG AACAAGCTGGAGAACGCAATATGATGAAATCAGCGAAAAGCCGCCGAG AACCCTCGCCCAATGCGGGTGGGGAGGAAAGGCGGAAAAGCCCGAAGG GCTTTAAAAATATTATTACGGTGTTAGCATAAAAACCTGTACCAATG  (1..287) ParE1Forward SEQ ID NO: 16 GGTCGTGTGGAAGGAACCCGGGAACTGGTTATTCACCCCCATTTTGTT CTGGTTTATGAGGTCGACAGCCAGTGGGGAAAAGTGTATGTCCTGCGC GTGTTGCATACCGCACAGAAGTGGCCATAAAATTCCAGTCAGGAATAA TACTTTTCATTTTTAGTTTACTGCTCCCCCAGTAAGAGCGATATATTC CGAACAGTCTTGTCTGGGAGGTATGGTGCAGTCAGCGAAGAACCGCCG AGAATCCTCGCCCAATGCGGGCGGGGAGCAGTCACCGGAGTCTTCGCC ACCCGCCCTCTGTGCACTGACCGGGTGATCCTGTCAGTGAGCGTGGTT CTGCCACTTCATCCGAATTCTTTCTTCCAGTTTGCTATGCAATCCGCC TCCGATCCACTGGCTGACCAGAGCTGCTGTTGCAAATGAACAGAAAGT CAAGGCGAATCCATGTTTAAACGTCTCCGGTAGTTCCTGGCCGGCGTG CTGAGTGATGATGGAAAACCCTATATATATAATAAAGGTACAAAAAAT TCCTGTGTGGGCGAGCCAGGCAAACCATTTGGCCACCCTGTATAACCC GTATTTCAATGGCATCTCCCGTTTAATATCATGAATAATCATTGTATC TATCTTGTGGGTCAGAGATTGAAATTTTGTAAATATCATAAGTCCTTA GTCCATCTAAAGTGAGATTTACCGTATCTGAATATATCAAAATGCTAA GGCAGAATCCCCGGAAATTTGTGTATTACTTCTGTAGCAGACACGGCA AAATCGTTGCATTACAGGTGCATCTGCTGGGGCATCTGTTTATCGATG CATCAGATTTAATGTCTGACAGTTACTTTTCTGTATCACCCACACTCT CTGCTTTTTCATTGCTACTGTCATATTTATGTCTGTTGCGCGGTTTTA TCTGTGTATATAAAATACATCTGTATTCATTGTTTTCTAAAAATTTGC GTATGTTGATAAAAAATCCGATTTCTTATTTCCATATTGGCACGTTTT TATTTTCAGGAAAAAAACGTCATCTTCTGGAATACTGGAAAGCAGAAG TTATCATGCGGGATAAGTTTGTTTTTCA (1..1084) ParE1 Reverse SEQ ID NO: 17 CCACATAAATCCGCAAACAAAAAACTTTAAGAAGCTGCAAACCTGAAA CAGCAAACCTGCAATATAGTCTTAACCCCATTATTTAATCCCCTGCGT TGCTTCGCCGCAGGGAAAGTCTTTATCTCTGAAACCACTGTGAACAAA CACAAAGAGGCCTTCGCTTGCAGCGGCCAAGGCCGCGCCGCTCAGAAT CTAAAAGCACCTCCCACGCTAACGCGCGGGCCCCGAACCTCACCGTTC TGAAACCACCGCGAAAACATCAGGAATAAAAAACACCACACAAACGCA GCACCGTGCCCACCCCTCATAACTGAAAAGCGAGGCCGCCCCCGCCCG AAGGGCGGGAACAACATCGCTTTTAATTATGAATGTTGTAACTACATT GTCATCGCTGCCAGTCTTCTGGCTGGAAGTCCTCAGTACACGCTCGTA AGCGGCCCTCACGGCCCGCTAACGCGGAGATACGCCCCGACTTCGGGT AAACCCTCGTCGGGACCACTCCGACCGCGCACAGAAACTGTCTCATGG CTGAAAGCGGGTATGGCTTAGCAGGGCTGGGGATGGGTAAGGTGAAAT CTATCAATCAGTACCGGCTGACGCCGGGCTTCGGCGGTTTTACTCCGG TATCACATGTAACCACAGCGTGCCGCCTTCCATGCCGCTGGCGCGGCA TATCCTGGTGACGATATCTGAATCGTTATATACTGTGTATACGTAGTA ATGACGAGGTGATAAATGGCACAGGTTAATATGAGTTTAAGAATCGAC GCTGAACTGAAGGATGCTTTTATGGCCGCTGCAAAAAGCATGGACCGT AATGGCTCTCAGTTAATTCGGGATTTTATGCGCCAGACCGTTGAACGG CAGCATAATACCTGGTTCCGTGAACAGGTTGCGGCAGGACGTCAGCAA CTCGAGCGCGGCGATGTGCTTCCCCATGACATGGTCGAATCTTCTGCC GCTGCATGGCGGGATGAAATGAGCAGGAAGGTTTCCGATAAATGATGG AGATATTCTGGACCATGCTGGCCAGCCAGGACAGGAAGCGCATTCGTG AGTAC (1..1061) TraA1 Reverse SEQ ID NO: 18 GAGATACTGATATTGTGCTTTTGTCAGCCATATGCTGGAAGCCGCATT CAGCTCTTCCCTGGCTCCCGGATTTAGCACAGGGTCCGGGTAAATCTT CATTAATCCATCAACAATATCTTTATTGACGGGTTTTATTTCACCGCC AAACTTCACGAAATCAATGAAGGCGCTATGGCGACGTAATGCCGATAC TGGTTGAATGTCAAAATTAGCCAGAATAAAAAAGTACCCTGGAAAAAT AGCGAATATTCTTTCACGGTAACAGCACCTGGAGTCTGCCCGTCTTAT CTTTCTTGTTATTAATGGAGTCCATGGTACGACGTTTTGCTCATTCAG CCATGAGAATAAAGATTCTCTGTTTTTGCCGGCTGTATTATATTGCGC AAGATACCAGTTCCGGTTATTCAGGTGTTCTATATTCACGAAGTTCAA CGCTCCGCGCAAAACCGATCCATGATGGACGATTTTGCGATGTCAGGC GAATATGCTAAATCATATGTCTGAAGCAGTATCCAGCCCGTATCTGGA TAAACTGCAGTTCTGACAGGCATATAACCAGCAGACTCTAGTACGTTC TGTATCGGTGATTTGGCGAACTCACAGATAAAGAACGGCTAAGCACTA ATATCAGCAATACAGTGGCACAGTATTGTGATACGCGAAATAAAACAT CAGCACGTCAGTTCAGAGTAAGATCGCCATATATCGGGCATGAGCCAG ATACAAATAACTGGGACACCGTCTGAAGTGATTTGCTTTATTAAAGTA ACTTGTGCTTGGTGTTTATGTTTATCAATTTGGGATCGCCTGTAAAGT GCAAAATGCAATTTCCATGAAAGTGTCCCCTTTAATGGGGACACCTGT TCACATTTTTTCGTTTTCTTTAGCTGTATTGCTAATCATGAAAACGAA AGTTCGCATCAGCACAGCAGAGCGAAGTGCATCATATCCTTCCAGATT TAAATTC (1..967) 

What is claimed is:
 1. A feed composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof and an ingestible food product; wherein the composition comprises Lactobacillus crispatus WZ-12 or a derivative thereof in an amount sufficient for use as a probiotic treatment of a subject.
 2. The composition of claim 1, wherein the composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof comprises Lactobacillus crispatus WZ-12 or a derivative thereof in an amount from 1×10⁴ to 1×10⁷ colony forming units per milliliter.
 3. The composition of claim 1 or claim 2, wherein the probiotic treatment comprises reducing an amount of antibiotic resistant bacteria in a gut microbiota of the subject.
 4. The composition of claim 3, wherein the antibiotic resistant bacteria comprise drug resistant Escherichia coli.
 5. The composition of any one of claims 1-4, wherein the subject is a poultry or porcine subject.
 6. The composition of any one of claims 1-5, wherein the ingestible food product comprises a feedstuff.
 7. The composition of any one of claims 1-5, wherein the ingestible food product comprises a nutritional supplement.
 8. The composition of any one of claims 1-7, further comprising one or more probiotic bacteria comprising Lactobacillus salivarius 1-14 or a derivative thereof, Lactobacillus salivarius 1-31 or a derivative thereof and Lactobacillus reuteri 2-2 or a derivative thereof.
 9. A composition comprising two or more probiotic bacteria comprising Lactobacillus crispatus WZ-12, Lactobacillus salivarius 1-14, Lactobacillus salivarius 1-31, and Lactobacillus reuteri 2-2 or a derivative thereof; and an excipient, diluent, or carrier; wherein the composition comprises the two or more probiotic bacteria in an amount sufficient for use as a probiotic treatment of a subject.
 10. The composition of claim 9, wherein the two or more probiotic bacteria are individually present in an amount from 1×10⁴ to 1×10⁷ colony forming units per milliliter.
 11. The composition of claim 9 or claim 10, wherein the probiotic treatment comprises reducing the amount of antibiotic resistant bacteria in a gut microbiota of the subject.
 12. The composition of any one of claims 9-11, wherein the subject is poultry or porcine.
 13. A pharmaceutical composition comprising the composition of any one of claims 9-12.
 14. An ingestible food product comprising the composition of any one of claims 9-12.
 15. A method of modulating gut microbiota in a subject comprising administering a composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof to the subject.
 16. The method of claim 15, wherein the composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof is administered with an ingestible food product.
 17. The method of claim 16, further comprising combining the composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof with the ingestible food product by spraying the composition onto the ingestible food product, or mixing or embedding the composition with or in the ingestible food product.
 18. The method of claim 16 or claim 17, wherein the ingestible food product comprises a feedstuff.
 19. The method of any one of claims 15-18, further comprising administering one or more probiotic bacteria comprising Lactobacillus salivarius 1-14 or a derivative thereof, and Lactobacillus reuteri 2-2 or a derivative thereof.
 20. The method of any one of claims 15-19, further comprising determining a reduced amount of antibiotic resistant bacteria in a gut microbiota of the subject after the administration step.
 21. The method of claim 20, wherein the determining step comprises measuring an amount of bla_(CMY-2) or other antibiotic resistance gene(s) in a fecal sample of the subject.
 22. The method of any one of claims 15-21, wherein the composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof is administered in two or more doses.
 23. The method of any one of claims 15-22, wherein the composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof is administered within one week of birth of the subject.
 24. A bacterial strain comprising a Lactobacillus crispatus WZ-12, Lactobacillus salivarius 1-14, or Lactobacillus reuteri 2-2 derivative engineered to comprise a derivative genome which differs from a parental genome of the parental strain by at least one nucleotide, and which improves one or more probiotic qualities of the engineered bacterial strain compared to the parental strain.
 25. The bacterial strain of claim 24, wherein the derivative lacks a mobile genetic element present in the parental strain.
 26. The bacterial strain of claim 25, wherein the mobile genetic element comprises a phage polynucleotide or an integron polynucleotide encoding one or more polypeptides capable of facilitating horizontal gene transfer.
 27. The bacterial strain of any one of claims 24-26, wherein the derivative lacks a polynucleotide encoding an antibiotic resistance polypeptide present in the parental strain.
 28. The bacterial strain of any one of claims 24-27, wherein the derivative comprises a polynucleotide having at least 90% identity to Lactobacillus crispatus WZ-12.
 29. The bacterial strain of any one of claims 24-28, wherein the improved quality comprises increased modulation of a gut microbiota in a subject as compared to the parental strain.
 30. The bacterial strain of claim 29, wherein the increased modulation comprises colonizing the gut microbiota of the subject for a greater duration than the parental strain.
 31. The bacterial strain of claim 29 or claim 30, wherein the increased modulation comprises reducing the amount of antibiotic resistant bacteria in the gut microbiota of the subject more than the parental strain.
 32. The bacterial strain of claims 29-31, wherein the increased gut modulation comprises an increase in population size or abundance of beneficial gut microorganisms.
 33. The bacterial strain of claim 32, wherein the beneficial gut microorganisms comprise Firmicutes and Cynobacteria.
 34. The composition of claim 4, wherein the E. coli is multidrug resistant.
 35. The composition of claim 4 or 31, wherein the E. coli is ampicillin resistant.
 36. A probiotic composition comprising the E. coli strain M9-4-1.
 37. A feed composition comprising Lactobacillus crispatus WZ-12 or a derivative thereof and E. coli strain M9-4-1 or a derivative thereof and an ingestible food product; wherein the composition comprises Lactobacillus crispatus WZ-12 or a derivative thereof and E. coli strain M9-4-1 or a derivative thereof in an amount sufficient for use as a probiotic treatment of a subject. 